Vaxcyte, Inc.

825 Industrial Road

Suite 300

San Carlos, California 94070

NOTICE OF ANNUAL MEETING OF STOCKHOLDERS

TO BE HELD AT 8:30 A.M. PACIFIC TIME ON THURSDAY, JUNE 12, 2025

Dear Stockholder:

You are cordially invited to attend the virtual Annual Meeting of Stockholders (the “Annual Meeting”) of Vaxcyte, Inc., a Delaware corporation (the “Company”). The Annual Meeting will be held on Thursday, June 12, 2025 at 8:30 a.m. Pacific Time via live webcast for the following purposes:

These items of business are more fully described in the Proxy Statement accompanying this notice.

This year’s Annual Meeting will be accessible through the internet via a live webcast. You will be able to attend the virtual Annual Meeting as well as vote during the meeting by visiting www.virtualshareholdermeeting.com/PCVX2025 and entering the 16-digit number included in your proxy card. Please refer to the additional logistical details and recommendations in the accompanying proxy statement.

The record date for the Annual Meeting is April 14, 2025. Only stockholders of record at the close of business on that date may vote at the Annual Meeting or any adjournment thereof. A complete list of stockholders entitled to vote at the Annual Meeting may be accessed electronically, upon request, starting ten days prior to the Annual Meeting by contacting Vaxcyte investor relations via email at investors@vaxcyte.com.

Your vote is important. Whether or not you expect to attend our Annual Meeting, please vote as soon as possible. We appreciate your continued support of the Company.

By the order of the Board of Directors,

/s/ Mikhail Eydelman

Senior Vice President, General Counsel, Chief Compliance Officer and Corporate Secretary

San Carlos, California

TABLE OF CONTENTS

Special Note Regarding Forward-Looking Statements

This proxy statement contains forward-looking statements about us and our industry that involve substantial risks and uncertainties. All statements other than statements of historical facts contained in this report, including statements regarding our future results of operations or financial condition, business strategy and plans and objectives of management for future operations, are forward-looking statements. In some cases, you can identify forward-looking statements because they contain words such as “anticipate,” “believe,” “contemplate,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “plan,” “potential,” “predict,” “project,” “seek,” “should,” “target,” “will,” or “would,” or the negative of these words or other similar terms or expressions.

Actual events or results may differ from those expressed in forward-looking statements. You should not rely on forward-looking statements as predictions of future events. We have based the forward-looking statements contained in this proxy statement primarily on our current expectations and projections about future events and trends that we believe may affect our business, financial condition and operating results. The outcome of the events described in these forward-looking statements is subject to risks, uncertainties and other factors described in the section titled “Risk Factors” in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024 filed with the Securities and Exchange Commission and other subsequent documents we file with the Securities and Exchange Commission. The Company expressly disclaims any obligation to update or alter any statements as a result of new information, future events or otherwise, except as required by law.

VAXCYTE, INC.

825 Industrial Road

Suite 300

San Carlos, California 94070

PROXY STATEMENT

FOR THE 2025 ANNUAL MEETING OF STOCKHOLDERS

TO BE HELD AT 8:30 A.M. PACIFIC TIME

ON THURSDAY, JUNE 12, 2025

QUESTIONS AND ANSWERS ABOUT THESE PROXY MATERIALS AND VOTING

Why did I receive a notice regarding the availability of proxy materials on the internet?

Pursuant to rules adopted by the Securities and Exchange Commission (the “SEC”), we have elected to provide access to our proxy materials over the internet. Accordingly, we have sent you a Notice of Internet Availability of Proxy Materials (the “Notice”) because the Board of Directors of Vaxcyte, Inc. (sometimes referred to as the “Company” or “Vaxcyte”) is soliciting your proxy to vote at the 2025 Annual Meeting of Stockholders (the “Annual Meeting”), including at any adjournments or postponements of the Annual Meeting. All stockholders will have the ability to access the proxy materials on the website referred to in the Notice or request to receive a printed set of the proxy materials. Instructions on how to access the proxy materials over the internet or to request a printed copy may be found in the Notice.

Will I receive any other proxy materials by mail?

No, you will not receive any other proxy materials by mail unless you request a paper copy of proxy materials. To request that a full set of the proxy materials be sent to your specified postal address, please go to www.proxyvote.com or call 1-800-579-1639. Please have your proxy card in hand when you access the website or call and follow the instructions provided.

How do I attend the Annual Meeting?

This year’s Annual Meeting will be accessible through the internet via a live webcast. You are entitled to participate in the Annual Meeting if you were a stockholder as of the close of business on our record date of April 14, 2025 or hold a valid proxy for the meeting. We have structured our virtual Annual Meeting to provide stockholders the same rights as if the meeting were held in person, including the ability to vote shares electronically during the meeting and ask questions in accordance with the rules of conduct for the meeting.

You will be able to attend the virtual Annual Meeting as well as vote during the meeting by visiting www.virtualshareholdermeeting.com/PCVX2025 and entering the 16-digit number included in your proxy card.

Beneficial stockholders who do not have a control number may gain access to the meeting by logging into their broker, brokerage firm, bank or other nominee’s website and selecting the stockholder communications mailbox to link through to the Annual Meeting; instructions should also be provided on the voting instruction card provided by your broker, bank or other nominee.

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If you have any technical difficulties or any questions regarding the virtual meeting website, please call the support team at the numbers listed on the log-in screen. If there are any technical issues in convening or hosting the meeting, we will promptly post information to the Investors & Media section of our website, http://investors.vaxcyte.com, including information on when the meeting will be reconvened.

We will provide our stockholders the opportunity to ask questions and make statements about a proposal during the formal business of the meeting. Questions and comments of a general nature will be held until after the conclusion of the formal business of the Annual Meeting. Instructions for submitting questions and making statements will be posted on the virtual meeting website. This live question and answer session will be conducted in accordance with certain Rules of Conduct. These Rules of Conduct will be posted on our Investors & Media website prior to the date of the Annual Meeting, and may include certain procedural requirements, such as limiting repetitive or follow-up questions, so that more stockholders will have an opportunity to ask questions. Out of consideration for other stockholders, we request that stockholders limit questions and comments to one and time to two minutes or less. This will allow every stockholder who wishes to speak an opportunity to do so.

Who can vote at the Annual Meeting?

Only stockholders of record at the close of business on April 14, 2025 will be entitled to vote at the Annual Meeting. On this record date, there were 128,999,351 shares of our common stock outstanding and entitled to vote.

Stockholders of Record: Shares Registered in Your Name

If on April 14, 2025 your shares were registered directly in your name with our transfer agent, Equiniti Trust Company, LLC, then you are a stockholder of record. As a stockholder of record, you may vote at the Annual Meeting if you attend online, vote by proxy through the internet or by telephone or vote by proxy using a proxy card that you may request or that we may elect to deliver at a later time. Whether or not you plan to attend the Annual Meeting, we encourage you to vote by proxy through the internet or by telephone as instructed below, or by completing a proxy card that you may request.

Beneficial Owners: Shares Registered in the Name of a Broker or Bank

If on April 14, 2025 your shares were held in an account at a brokerage firm, bank, dealer or other similar organization, then you are the beneficial owner of shares held in “street name” and the Notice is being forwarded to you by that organization. The organization holding your account is considered to be the stockholder of record for purposes of voting at the Annual Meeting. As a beneficial owner, you have the right to direct your broker or other agent regarding how to vote the shares in your account. As a beneficial owner, you are also invited to attend the Annual Meeting. However, since you are not the stockholder of record, you may not vote your shares online at the Annual Meeting unless you request and obtain a valid proxy from your broker, bank, dealer or other agent.

What is the quorum requirement?

A quorum of stockholders is necessary to hold a valid meeting. A quorum will be present if the holders of a majority of the voting power of the outstanding shares entitled to vote are electronically present online at the meeting or represented by proxy. On the record date, there were 128,999,351 shares of common stock outstanding and entitled to vote. Thus, the holders of 64,499,676 shares must be present online or represented by proxy at the Annual Meeting to have a quorum.

Your shares will be counted towards the quorum only if you submit a valid proxy (or one is submitted on your behalf by your broker, bank or other agent) or if you attend the Annual Meeting. Abstentions and broker non-votes will be counted towards the quorum requirement. If there is no quorum, the holders of a majority of shares electronically present online at the Annual Meeting or represented by proxy may adjourn the meeting to another date.

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What am I voting on?

There are four proposals scheduled for a vote at the Annual Meeting:

Proposal No. 1: To elect the three nominees for Class II director named herein to hold office until our 2028 Annual Meeting of Stockholders and until their successors have been duly elected and qualified.

Proposal No. 2: To ratify the appointment of Deloitte & Touche LLP as our independent registered public accounting firm for the fiscal year ending December 31, 2025.

Proposal No. 3: Advisory approval of the compensation of our named executive officers.

Proposal No. 4: Approval of the amendment and restatement of our Amended and Restated Certificate of Incorporation to provide for officer exculpation as permitted by recent amendments to the Delaware General Corporation Law.

What if another matter is properly brought before the meeting?

We are not aware of any other matters that will be presented for stockholder action at the Annual Meeting. If other matters are properly introduced, the persons named in the accompanying proxy will vote the shares of our common stock they represent according to their judgment.

How do I vote?

For Proposal No. 1, election of Class II directors, you may either vote “For” the nominees to the Board of Directors or you may “Withhold” your vote for any nominee you specify.

For Proposal No. 2, to ratify the appointment of Deloitte & Touche LLP as our independent registered public accounting firm, you may vote “For” or “Against” or “Abstain” from voting.

For Proposal No. 3, advisory approval of the compensation of our named executive officers, you may vote “For” or “Against” or “Abstain” from voting.

For Proposal No. 4, approval of the amendment and restatement of our Amended and Restated Certificate of Incorporation to provide for officer exculpation as permitted by recent amendments to the Delaware General Corporation Law, you may vote “For” or “Against” or “Abstain” from voting.

Stockholders of Record: Shares Registered in Your Name

If you are a stockholder of record, there are several ways for you to vote your shares. Whether or not you plan to attend the Annual Meeting, we urge you to vote by proxy to ensure that your vote is counted. You may still attend the Annual Meeting and vote electronically during the meeting even if you have already voted by proxy.

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Beneficial Owners: Shares Registered in the Name of Broker or Bank

If you are a beneficial owner of shares registered in the name of your broker, bank or other agent, you should have received a Notice containing voting instructions from that organization rather than directly from us.

Regarding internet proxy voting, please be aware that you must bear any costs associated with your internet access, such as usage charges from internet access providers and cellular companies.

Can I change my vote after submitting my proxy?

Stockholder of Record: Shares Registered in Your Name

Yes. You can revoke your proxy at any time before the final vote at the Annual Meeting. If you are the record holder of your shares, you may revoke your proxy in any one of the following ways:

Your most current proxy card or telephone or internet proxy is the one that is counted.

Beneficial Owner: Shares Registered in the Name of Broker or Bank

If your shares are held by your broker, bank or other agent, you should follow the instructions provided by your broker, bank or other agent to change your vote.

How many votes do I have?

On each matter to be voted upon, each share of our common stock that you own as of April 14, 2025 entitles you to one vote.

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What does it mean if I receive more than one Notice?

If you receive more than one Notice, your shares may be registered in more than one name or in different accounts. Please follow the voting instructions on each of the Notices you receive to ensure that all of your shares are voted.

If I am a stockholder of record and I do not vote, or if I return a proxy card or otherwise vote without giving specific voting instructions, what happens?

If you are a stockholder of record and do not vote by completing a proxy card, by telephone, through the internet or online at the Annual Meeting, your shares will not be voted.

If you return a signed and dated proxy card or otherwise vote without marking voting selections, your shares will be voted, as applicable, “For” Proposal No. 1 to elect the three nominees for director; “For” Proposal No. 2 to ratify the appointment of Deloitte & Touche LLP as the Company’s independent registered public accounting firm; “For” Proposal No. 3 for the advisory approval of executive compensation; and “For” Proposal No. 4 for the approval of the amendment and restatement of our Amended and Restated Certificate of Incorporation to provide for officer exculpation as permitted by recent amendments to the Delaware General Corporation Law. If any other matter is properly presented at the meeting, your proxyholder will vote your shares using his or her best judgment.

If I am a beneficial owner of shares held in street name and I do not provide my broker, bank or other agent with voting instructions, what happens?

If you are a beneficial owner of shares held in street name and you do not instruct your broker, bank or other agent on how to vote your shares, your broker, bank or other agent may still be able to vote your shares in its discretion. In this regard, under the rules of the listing requirements of the Nasdaq Global Select Market (“Nasdaq”), brokers, banks and other securities intermediaries that are subject to Nasdaq rules may use their discretion to vote your “uninstructed” shares with respect to matters considered to be “routine” under Nasdaq rules, but not with respect to “non-routine” matters. In this regard, Proposals No. 1, 3 and 4 are considered to be “non-routine” matters under Nasdaq rules, meaning that your broker may not vote your shares on Proposals No. 1, 3 and 4 in the absence of your voting instructions. However, Proposal No. 2, to ratify the appointment of Deloitte & Touche LLP as the Company’s independent registered public accounting firm, is considered to be a “routine” matter under Nasdaq rules, meaning that if you do not return voting instructions to your broker by its deadline, your shares may be voted by your broker, bank or other agent in its discretion on Proposal No. 2.

If you are a beneficial owner of shares held in street name, in order to ensure your shares are voted in the way you would prefer, you must provide voting instructions to your broker, bank or other agent by the deadline provided in the materials you receive from your broker, bank or other agent.

How many votes are needed to approve each proposal?

Proposal No. 1: Directors will be elected by a plurality of the votes cast, meaning that the three nominees who receive the most “For” votes from the holders of shares present online or represented by proxy and entitled to vote on the election of directors will be elected. Accordingly, only votes “For” will affect the outcome.

Proposal No. 2: To ratify the appointment of Deloitte & Touche LLP as our independent registered public accounting firm for the fiscal year ending December 31, 2025, the proposal must receive “For” votes from the holders of a majority of shares present online or represented by proxy and entitled to vote on the matter. If you “Abstain” from voting, it will have the same effect as an “Against” vote.

Proposal No. 3: This proposal, commonly referred to as the “say-on-pay” vote, must receive “For” votes from the holders of a majority shares present online or represented by proxy and entitled to vote on the matter. Since this proposal is an advisory vote, the result will not be binding on our Board of Directors. However, our Board of

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Directors values our stockholders’ opinions, and our Board of Directors and the Compensation Committee will take into account the outcome of the advisory vote when considering future executive compensation decisions.

Proposal No. 4: To approve the amendment and restatement of our Amended and Restated Certificate of Incorporation to provide for officer exculpation as permitted by recent amendments to the Delaware General Corporation Law, the proposal must receive “For” votes from holders of at least 66 2/3% of the outstanding shares of our common stock as of April 14, 2025.

How are votes counted?

Votes will be counted by the inspector of election appointed for the meeting, who will separately count, for:

For Proposal No. 1, the election of directors is determined by a plurality of votes cast, so a “Withhold” vote and broker non-votes will not be counted in determining the outcome of such proposal.

For Proposal No. 2, to ratify the appointment of Deloitte & Touche LLP as the Company’s independent registered public accounting firm, abstentions and broker non-votes will be counted towards the vote total and will have the same effect as “Against” votes. As explained below, broker non-votes are not expected on this proposal.

For Proposal No. 3, advisory approval of the compensation of our named executive officers, abstentions will be counted towards the vote total and will have the same effect as “Against” votes. Broker non-votes have no effect and will not be counted towards the vote total for this proposal.

For Proposal No. 4, approval of the amendment and restatement of our Amended and Restated Certificate of Incorporation to provide for officer exculpation as permitted by recent amendments to the Delaware General Corporation Law, abstentions and broker non-votes will be counted towards the vote total and will have the same effect as “Against” votes.

What are “broker non-votes”?

As discussed above, when a beneficial owner of shares held in street name does not give voting instructions to his or her broker, bank or other securities intermediary holding his or her shares as to how to vote on matters deemed to be “non-routine” under Nasdaq rules, the broker, bank or other such agent cannot vote the shares. These unvoted shares are counted as “broker non-votes.” Since Proposals No. 1, 3 and 4, are considered to be “non-routine” matters under Nasdaq rules, we expect broker non-votes to exist in connection with Proposals No. 1, 3 and 4. Proposal No. 2, to ratify the appointment of Deloitte & Touche LLP as the Company’s independent registered public accounting firm, is considered to be a “routine” matter under Nasdaq rules, and therefore we do not expect broker non-votes to exist in connection with Proposal No. 2.

As a reminder, if you are a beneficial owner of shares held in street name, in order to ensure your shares are voted in the way you would prefer, you must provide your voting instructions to your broker, bank or other agent by the deadline provided in the materials you receive from your broker, bank or other agent.

Who is paying for this proxy solicitation?

We will pay for the entire cost of soliciting proxies. In addition to these proxy materials, our directors and employees may also solicit proxies in person, or by other means of communication. Directors and employees will

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not be paid any additional compensation for soliciting proxies. We may also reimburse brokerage firms, banks and other agents for the cost of forwarding proxy materials to beneficial owners.

How can I find out the results of the voting at the Annual Meeting?

Preliminary voting results will be announced at the Annual Meeting. In addition, final voting results will be published in a current report on Form 8-K that we expect to file within four business days after the Annual Meeting. If final voting results are not available to us in time to file a Form 8-K within four business days after the Annual Meeting, we intend to file a Form 8-K to publish preliminary results and, within four business days after the final results are known to us, file an additional Form 8-K to publish the final results.

When are stockholder proposals and director nominations due for next year’s annual meeting?

To be considered for inclusion in our proxy materials for our 2026 Annual Meeting of Stockholders, your proposal (including any director nominations) must be submitted in writing by December 29, 2025 to our Corporate Secretary at 825 Industrial Road, Suite 300, San Carlos, California 94070, and you must comply with all applicable requirements of Rule 14a-8 promulgated under the Securities Exchange Act of 1934, as amended (the “Exchange Act”). However, if the 2026 Annual Meeting of Stockholders is advanced by more than 30 days prior to or delayed by more than 30 days after June 12, 2026, then the deadline will be a reasonable time prior to the time we begin to print and send our proxy materials.

Pursuant to our Amended and Restated Bylaws (our “Bylaws”), if you wish to submit a proposal (including a director nomination) at the 2026 Annual Meeting of Stockholders that is not to be included in next year’s proxy materials, you must do so not later than the close of business on March 14, 2026 and no earlier than the close of business on February 12, 2026; provided, however, that if next year’s annual meeting is advanced by more than 30 days prior to or delayed by more than 30 days after June 12, 2026, your proposal must be submitted not earlier than the close of business on the 120^th day prior to such annual meeting and not later than the close of business on the 90^th day prior to such annual meeting or the 10^th day following the day on which public announcement of such meeting is first made. You are advised to review our Bylaws, which contain additional requirements about advance notice of stockholder proposals and director nominations. In addition, the proxy solicited by our Board of Directors for the 2026 Annual Meeting will confer discretionary voting authority with respect to (i) any proposal presented by a stockholder at that meeting for which the Company has not been provided with timely notice and (ii) any proposal made in accordance with our Bylaws, if the 2026 proxy statement briefly describes the matter and how management proxy holders intend to vote on it, if the stockholder does not comply with the requirements of Rule 14a-4(c)(2) promulgated under the Exchange Act.

In addition, stockholders who intend to solicit proxies in support of director nominees other than the Company’s nominees must comply with Rule 14a-19 under the Exchange Act.

What proxy materials are available on the internet?

The proxy statement and annual report to stockholders are available at www.proxyvote.com.

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PROPOSAL NO. 1

ELECTION OF DIRECTORS

Our Board of Directors is divided into three classes. We currently have three directors in Class I, four directors in Class II and two directors in Class III. Each class serves for a three-year term. Vacancies on the Board of Directors may be filled only by persons elected by a majority of the remaining directors unless the Board of Directors determines by resolution that any such vacancies will be filled by stockholders. A director elected by the Board of Directors to fill a vacancy in a class, including vacancies created by an increase in the number of directors, will serve for the remainder of the full term of that class and until the director’s successor is duly elected and qualified, or, if sooner, until the director’s death, resignation or removal. Proxies cannot be voted for a greater number of persons than the number of nominees named.

The Board of Directors presently has nine directors. Peter Hirth will be retiring from the Board of Directors as of the 2025 Annual Meeting and has not been re-nominated as a director. Dr. Hirth’s position as a member of the Board of Directors will end upon the expiration of his current term at the Annual Meeting, and, as a result, following the Annual Meeting, the size of the Board of Directors will be reduced to eight directors.

If elected at the Annual Meeting, these nominees would serve until the 2028 Annual Meeting of Stockholders and until their successors have been duly elected and qualified, or, if sooner, until the director’s death, resignation or removal.

Directors are elected by a plurality of the votes of the holders of shares present at the Annual Meeting or represented by proxy and entitled to vote on the election of directors. Accordingly, the nominees receiving the highest number of affirmative votes will be elected. Shares represented by executed proxies will be voted, if authority to do so is not withheld, for the election of each of the nominees named below. If any nominee becomes unavailable for election as a result of an unexpected occurrence, shares that would have been voted for that nominee instead will be voted for the election of a substitute nominee proposed by the Company. Each person nominated for election has consented to being named as a nominee in this proxy statement and has agreed to serve if elected. We have no reason to believe that any nominee will be unable to serve.

Our policy is to encourage directors and nominees for director to attend the Annual Meeting. All but two of our directors attended the 2024 Annual Meeting, which was held virtually.

Class II Director Nominees for Election for a Three-Year Term Expiring at the 2028 Annual Meeting

John Furey. Mr. Furey, 60, has served on our Board of Directors since July 2024. Mr. Furey has served as Chief Executive Officer and a member of the board of directors of Imvax, Inc., a privately held clinical-stage biotechnology company, since September 2019, and as a member of the board of directors of Adaptimmune

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Therapeutics plc, a publicly traded clinical-stage biopharmaceutical company, since July 2018. Mr. Furey previously served as member of the board of directors of Sensorion SA, a privately held clinical-stage biopharmaceutical company, from August 2019 to April 2025, and as the Chief Operating Officer of Spark Therapeutics, Inc., a publicly traded biotechnology company, from December 2016 to January 2019. Prior to joining Spark Therapeutics, Mr. Furey served as the senior vice president and head of global operations at Baxalta, a spin off company of Baxter International. Earlier in his career, he held both commercial and operations positions of increasing scope and responsibility with Wyeth Pharmaceuticals, Pfizer and Baxter. Mr. Furey holds an executive M.B.A. from St. Joseph’s University, Philadelphia, a B.S. from Trinity College, Dublin, and a diploma in Environmental Health from the Technological University, Dublin. Mr. Furey was selected to serve on our Board of Directors for his more than 30 years of experience in developing and implementing operational strategies and leading commercial and technical teams.

Jacks Lee. Mr. Lee, 61, has served on our Board of Directors since November 2023. Mr. Lee is currently President and owner of JL Innovative Transformations LLC, an advisory and consultancy company that he founded in June 2022. Mr. Lee previously served as a member of the board of directors of G1 Therapeutics, Inc., a publicly traded biopharmaceutical company, from June 2022 to September 2024 when it was acquired by Pharmacosmos A/S. Mr. Lee held various roles at Merck & Co., Inc., a publicly traded multinational pharmaceutical company, from 2007 to June 2023, where he most recently served as Senior Vice President of Global Manufacturing & Supply from 2014 until June 2023. Previously, Mr. Lee held various roles of increasing responsibility with Sanofi Aventis and its predecessor companies from 1988 to 2007, including Head of Manufacturing Global Pharmaceutical Products from 2002 to 2004 and Head of Manufacturing Vaccines and Biologics from 2004 to 2007. Mr. Lee holds an M.S. in Industrial Management from the University of Central Missouri and earned his B.S. in Industrial Engineering at the University of Wisconsin—Madison. Mr. Lee was selected to serve on our Board of Directors for his more than 30 years of experience having led global strategic supply and manufacturing operations at leading multi-national pharmaceutical companies, with a significant focus on vaccines and biopharmaceuticals.

Heath Lukatch, Ph.D. Dr. Lukatch, 57, has served on our Board of Directors since May 2018. Dr. Lukatch has served as Founder and Managing Partner of Red Tree Venture Capital, a life sciences venture capital firm, since March 2020. Dr. Lukatch currently serves as a member of the boards of directors of numerous privately held companies, including Engrail Therapeutics, since March 2024, Acrigen Biosciences, where he is board chair, since July 2021, Excellergy Therapeutics since January 2021 and Magnus Medical, Inc., where he is board chair, since December 2020. From 2015 to 2020, Dr. Lukatch held various roles at TPG, Inc., a private equity firm, including Partner and Managing Director, TPG Biotech from May 2015 to December 2017 and Partner, TPG Growth and RISE from January 2018 to March 2020. In 2006, Dr. Lukatch co-founded Novo Ventures’ San Francisco office, where he was a Partner through 2015. Prior to joining Novo Ventures, Dr. Lukatch was a Managing Director responsible for biotechnology venture investments at Piper Jaffray Ventures and SightLine Partners. Dr. Lukatch previously served as a chairman of the boards of directors of Inogen, Inc., a publicly traded medical technology company, from December 2006 to March 2022, of Engage Therapeutics, Inc., a privately held pharmaceutical company, from September 2017 to June 2020, when it was acquired by UCB, and Satsuma Pharmaceuticals, Inc., a publicly traded biopharmaceutical company, from December 2016 to June 2023. Dr. Lukatch also served as a member of the boards of directors of Bicara Therapeutics from July 2023 to September 2024, Virsti Therapeutics from April 2021 to April, 2023, Cargo Therapeutics, Inc. from January 2021 until its initial public offering in November, 2023, Flexion Therapeutics, Inc., a publicly traded biopharmaceutical company, from December 2012 to November 2021, when it was acquired by Pacira BioSciences, Inc., ViaCyte Inc. from November 2018 to December 2020, Ceribell. Inc. from September 2018 to December 2020, and Halo Neuroscience from November 2017 to October 2020. Prior to becoming an investor, Dr. Lukatch worked as a strategy consultant with McKinsey & Company and was co-founder and CEO of AutoMate Scientific, Inc., a biotechnology instrumentation company. In addition, Dr. Lukatch was a bench scientist at Chiron, Roche Bioscience and Cetus, doing molecular biology, electrophysiology and protein chemistry, respectively. Dr. Lukatch holds a B.A. with high honors in Biochemistry from the University of California at Berkeley and a Ph.D. in Neuroscience from Stanford University where he was a DOD USAF

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Fellow. Dr. Lukatch was selected to serve on our Board of Directors because of his extensive industry experience, his experience with venture capital investments and his experience of serving on the board of directors for several biopharmaceutical and healthcare companies.

THE BOARD OF DIRECTORS RECOMMENDS

A VOTE “FOR” EACH OF OUR NOMINEES NAMED ABOVE.

Class III Directors Continuing in Office Until the 2026 Annual Meeting

Halley Gilbert, J.D. Ms. Gilbert, 55, has served on our Board of Directors since April 2020. Ms. Gilbert has served as Chief Legal Officer of CARGO Therapeutics, Inc., a publicly traded biotechnology company, since September 2023. From August 2021 to May 2022, Ms. Gilbert served as Chief Legal Officer of Neogenomics, Inc., a publicly traded cancer diagnostics company. From June 2020 to August 2021, Ms. Gilbert served as Chief Operating Officer and Chief Business Officer at Adagio Therapeutics, Inc. From 2008 to February 2020, Ms. Gilbert served in various roles at Ironwood Pharmaceuticals, Inc., a biopharmaceutical company, including as Senior Vice President, Corporate Development and Chief Administrative Officer from March 2019 to February 2020, as Senior Vice President, Chief Legal Officer and Corporate Secretary from 2014 to March 2019 and as Vice President, General Counsel and Corporate Secretary from 2008 to 2014. Prior to joining Ironwood Pharmaceuticals, Ms. Gilbert was Vice President, Deputy General Counsel at Cubist Pharmaceuticals, Inc. and previously served as a corporate counsel at Genzyme Corp., prior to its acquisition by Sanofi. Ms. Gilbert began her career at Skadden, Arps, Slate, Meagher & Flom LLP, where she specialized in mergers and acquisitions and securities law. Ms. Gilbert has served as a member of the boards of directors of Arcutis Biotherapeutics, Inc., a publicly traded biopharmaceutical company, since May 2020 and of CytomX Therapeutics, Inc., a publicly traded biopharmaceutical company, since April 2020. From November 2019 to February 2020, Ms. Gilbert served on the board of directors of Dermira, Inc. (acquired by Eli Lilly and Company), a medical dermatology company. From January 2017 to April 2019, Ms. Gilbert served on the board of directors of Achaogen, Inc., a biopharmaceutical company. Ms. Gilbert holds a B.A. from Tufts University and a J.D. from Northwestern University School of Law. Ms. Gilbert was selected to serve on our Board of Directors because of the depth of her biotechnology industry management and operations expertise and public company board of directors experience.

Grant E. Pickering M.B.A. Mr. Pickering, 57, is our co-founder and has served as our Chief Executive Officer and as a member of our Board of Directors since November 2013. Mr. Pickering also served as our President from November 2013 until January 2021. From May 2013 to April 2015, Mr. Pickering served as Strategic Advisor at Atreca, Inc., a biotechnology company. Prior to joining Vaxcyte, Mr. Pickering was the Chief Executive Officer of Mymetics Corporation, a developer of virosomal vaccines for infectious diseases. Prior to that, Mr. Pickering was an Executive-in-Residence at Kleiner Perkins, a venture capital firm, and Senior Vice President of Operations of Dendreon Corporation, a biopharmaceutical company. Mr. Pickering served as the Chief Executive Officer and a director of Juvaris BioTherapeutics, Inc., a privately held biopharmaceutical company, from March 2008 to December 2023, and currently serves as a member of the board of directors of Athira Pharma, Inc., a publicly traded biopharmaceutical company, since January 2022. Mr. Pickering holds a B.S. in Marketing from Penn State University and an M.B.A. from Georgetown University. Mr. Pickering was selected to serve on our Board of Directors because of the perspective and experience he brings as our Chief Executive Officer and his operating and management experience in the healthcare industry.

Class I Directors Continuing in Office Until the 2027 Annual Meeting

Annie Drapeau. Ms. Drapeau, 58, has served on our Board of Directors since September 2021. Ms. Drapeau served as Chief People Officer of Toast, Inc., a publicly traded cloud-based restaurant management software company, from May 2019 to May 2024. From October 2016 to May 2019, Ms. Drapeau served as Chief People Officer of Moderna Therapeutics, Inc., a publicly traded pharmaceutical and biotechnology company. From April 2015 to October 2016, Ms. Drapeau served as Operating Partner of Bain Capital, a private investment firm.

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From March 2010 to March 2015, Ms. Drapeau served as Executive Vice President, Strategy and Talent for Iron Mountain Inc., a publicly traded enterprise information management services company. Additionally, Ms. Drapeau has served as Chief People Officer at VistaPrint and Digitas, and started her career in finance roles at JP Morgan and PepsiCo. Ms. Drapeau holds a B.S. in Chemical Engineering from Bucknell University, of which she is a current member of the Board of Trustees, and an M.B.A. from the Tuck School of Business at Dartmouth College. Ms. Drapeau was selected to serve on our Board of Directors because of the depth of her life sciences industry and operations expertise.

Teri Loxam. Ms. Loxam, 53, has served on our Board of Directors since September 2021. Ms. Loxam has served as Chief Financial Officer of Compass Pathways plc, a publicly traded biotechnology company, since March 2024, and as a member of the board of directors of Cardiol Therapeutics Inc., a publicly traded life sciences company, since May 2022. Ms. Loxam previously served as Chief Financial Officer of Gameto, a privately held biotechnology company, from April 2023 to October 2023, Chief Financial Officer and Chief Operating Officer of Kira Pharmaceuticals, a privately held biotechnology company, from November 2021 to March 2023, and Chief Financial Officer of SQZ Biotechnologies, a publicly traded biotechnology company, from September 2019 to November 2021. From August 2015 to August 2019, Ms. Loxam was at Merck & Co., Inc., a publicly traded multinational pharmaceutical company, where she served as Senior Vice President of Investor Relations and Global Communications. Before that, from July 2012 to August 2015, Ms. Loxam served as Vice President of Investor Relations at IMAX, an entertainment technology company. From June 2001 to July 2012, Ms. Loxam had a number of roles of increasing responsibility across Strategy, Treasury and Investor Relations at Bristol-Myers Squibb, a publicly traded multinational pharmaceutical company. Ms. Loxam holds an M.B.A. from the University of California, Irvine, Paul Merage School of Business, and a B.Sc. from the University of Victoria. Ms. Loxam was selected to serve on our Board of Directors because of the depth of her life sciences industry, investor relations and financial expertise.

Carlos Paya, M.D., Ph.D. Dr. Paya, 66, has served as a member and chairman of our Board of Directors since October 2021. Dr. Paya has served as a Venture Partner at Abingworth LLP (acquired by The Carlyle Group Inc.) since January 2020. Dr. Paya has also served as chairman of the board directors of Highlight Therapeutics S.L, a privately held immuno-oncology company, since January 2020. Additionally, Dr. Paya serves as a Senior Advisor to Ysios Capital, a privately held life sciences investor, and Launch Therapeutics, a privately held clinical development company. Dr. Paya previously served as a member of the boards of directors of Standard BioTools, Inc., a publicly traded biological research equipment company, from March 2017 to January 2024, where he also served as chairman from May 2020 to January 2024 when it merged with SomaLogic, Inc., and of Mallinckrodt Pharmaceuticals, a publicly traded pharmaceutical company, from May 2019 to June 2022, as well as president, chief executive officer and director of Immune Design Corp, a publicly traded therapeutic vaccines company, from May 2011 to May 2019 when it was acquired by Merck & Co., Inc. Dr. Paya previously served as president of Elan Corporation, a publicly traded pharmaceutical company, which was acquired by Perrigo Company, from November 2008 to April 2011. Before joining Elan Corporation, Dr. Paya served as Vice President of the Lilly Research Laboratories at Eli Lilly & Company, a publicly traded pharmaceutical company, from September 2001 to November 2008. From January 1991 to August 2001, Dr. Paya was professor of medicine, immunology, and pathology, and vice dean of the clinical investigation program at the Mayo Clinic in Rochester, Minnesota. Dr. Paya holds M.D. and Ph.D. degrees from the University of Madrid and underwent postdoctoral training at the Institute Pasteur, Paris, France. Dr. Paya was selected to serve on our Board of Directors because of his experience in the life sciences industry.

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CORPORATE GOVERNANCE AND BOARD MATTERS

Overview

We are committed to exercising good corporate governance practices. In furtherance of this commitment, we regularly monitor developments in the area of corporate governance and review our processes, policies and procedures in light of such developments. Key information regarding our corporate governance initiatives can be found on the Investors & Media section of our website, http://investors.vaxcyte.com, including our Corporate Governance Guidelines, our Code of Business Conduct and Ethics and the charters for our Audit, Compensation and Nominating and Corporate Governance Committees. We believe that our corporate governance policies and practices, including the substantial percentage of independent directors on our Board of Directors, empower our independent directors to effectively oversee our management—including the performance of our Chief Executive Officer—and provide an effective and appropriately balanced board governance structure.

Independence of the Board of Directors

As required under the Nasdaq listing standards, a majority of the members of a listed company’s board of directors must qualify as “independent,” as affirmatively determined by its board of directors.

Our Board of Directors has undertaken a review of the independence of each director. Based on information provided by each director concerning his or her background, employment and affiliations, our Board of Directors has determined that Annie Drapeau, John Furey, Halley Gilbert, Peter Hirth, Jacks Lee, Teri Loxam, Heath Lukatch, and Carlos Paya do not have relationships that would interfere with the exercise of independent judgment in carrying out the responsibilities of a director and that each of these directors is “independent” as that term is defined under applicable Nasdaq listing standards. In determining Ms. Gilbert’s independence, our Board of Directors considered our entry into a sublease agreement, dated July 1, 2024 (the “Sublease Agreement”) with CARGO Therapeutics, Inc. (“CARGO”), where Ms. Gilbert has served as Chief Legal Officer since September 2023. Our Board of Directors determined that execution of the Sublease Agreement did not affect Ms. Gilbert’s independence.

In addition, our Board of Directors has determined that each member of the Audit, Compensation and Nominating and Corporate Governance Committees meets the applicable Nasdaq and SEC rules and regulations regarding “independence” and that each member is free of any relationship that would interfere with his or her individual exercise of independent judgment with regard to the Company. In making these determinations, our Board of Directors considered the current and prior relationships that each non-employee director has with the Company and all other facts and circumstances our Board of Directors deemed relevant in determining their independence, including the beneficial ownership of our shares held by each non-employee director and the transactions described in the section titled “Certain Relationships and Related Person Transactions.” Mr. Pickering is not considered independent because he currently serves as our Chief Executive Officer.

Board Leadership Structure

Our Board of Directors is currently led by our Chairman, Carlos Paya. Our Board of Directors recognizes that it is important to determine an optimal board leadership structure to ensure the independent oversight of management as the Company continues to grow. We separate the roles of Chief Executive Officer and Chairman in recognition of the differences between the two roles. Our Chief Executive Officer is responsible for setting the strategic direction for the Company and the day-to-day leadership and performance of the Company, while our chairman provides guidance to our Chief Executive Officer and presides over meetings of the full Board of Directors. We believe that this separation of responsibilities provides a balanced approach to managing our Board of Directors and overseeing the Company.

Our Board of Directors has concluded that our current leadership structure is appropriate at this time. However, our Board of Directors will continue to periodically review our leadership structure and may make such changes in the future as it deems appropriate.

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Role of the Board of Directors in Risk Oversight

Our Board of Directors has responsibility to oversee the Company’s risk management processes. Our Board of Directors believes that risk management is an important part of establishing, updating and executing on our business strategy. Our Board of Directors, as a whole and at the committee level, regularly discusses with management major risks that could affect the corporate strategy, business objectives, compliance, operations and the financial condition and performance of the Company. Our Board of Directors focuses its oversight on the most significant risks facing the Company and on the Company’s processes to identify, prioritize, assess, manage and mitigate those risks. Our Board of Directors and its committees receive regular reports from members of the Company’s senior management on areas of material risk to the Company, including strategic, operational, financial, legal, regulatory, cyber and reputational risks.

Our Audit Committee is responsible for overseeing our financial reporting process on behalf of our Board of Directors. Our Audit Committee oversees and monitors risk management and reviews with management and our independent registered public accounting firm, as appropriate, our significant risk exposures and the actions management has taken to limit, monitor or control such exposures. Periodically, the Audit Committee reviews our policies, processes and controls with respect to risk assessment, risk management, loss prevention and regulatory compliance.

Our Compensation Committee is responsible for overseeing our practices and policies regarding talent acquisition, retention, development and compensation as they relate to risk management and risk-taking incentives to determine whether such policies and practices encourage excessive or inappropriate risk taking by employees.

Our Nominating and Corporate Governance Committee oversees the management of risks associated with our overall compliance and corporate governance practices and the independence and composition of our Board of Directors.

While each committee is responsible for evaluating certain risks and overseeing the management of such risks, the entire Board of Directors is regularly informed through committee reports about such risks. Matters of significant strategic risk are considered by our Board of Directors as a whole. While our Board of Directors and its committees have an oversight role, management is principally tasked with direct responsibility for management and assessment of risks and the implementation of processes and controls to mitigate their effects on the Company.

Meetings of the Board of Directors and its Committees

Our Board of Directors has an Audit Committee, a Compensation Committee and a Nominating and Corporate Governance Committee. The following table provides membership and meeting information for 2024 for the Board of Directors and each of its committees:

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The Board of Directors met 10 times during 2024. Each current director attended 75% or more of the aggregate number of meetings of the Board of Directors and of the committees on which he or she served, held during the portion of 2024 for which he or she was a director or committee member.

Director Skills and Qualifications

The following includes a skills and qualifications matrix highlighting many of the key experiences and competencies our directors bring to the Company.

Information Regarding Committees of the Board of Directors

Below is a description of our Audit Committee, Compensation Committee and Nominating and Corporate Governance Committee. The written charters of our committees are available to stockholders on the Investors & Media section of our website at http://investors.vaxcyte.com. Each of the committees has authority to engage legal counsel, consultants or other experts, as it deems appropriate to carry out its responsibilities.

Audit Committee

Our Audit Committee currently consists of Teri Loxam (Chairperson), Halley Gilbert and Jacks Lee, each of whom our Board of Directors has determined satisfies the independence requirements under the Nasdaq listing

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standards and Rule 10A-3(b)(1) of the Exchange Act. Our Board of Directors has determined that Ms. Loxam is an “audit committee financial expert” within the meaning of SEC regulations.

Each member of our Audit Committee can read and understand fundamental financial statements in accordance with applicable requirements. In arriving at these determinations, our Board of Directors has examined each Audit Committee member’s scope of experience and the nature of her or his employment.

The primary purpose of the Audit Committee is to discharge the responsibilities of our Board of Directors with respect to our corporate accounting and financial reporting processes, systems of internal control and financial statement audits, and to oversee our independent registered public accounting firm. Specific responsibilities of our Audit Committee include:

Report of the Audit Committee of the Board of Directors

The Audit Committee has reviewed and discussed the audited financial statements for the fiscal year ended December 31, 2024 with management of the Company. The Audit Committee has discussed with Deloitte & Touche LLP, the Company’s independent registered public accounting firm, the matters required to be discussed by the applicable requirements of the Public Company Accounting Oversight Board (the “PCAOB”) and the SEC. The Audit Committee has also received the written disclosures and the letter from Deloitte & Touche LLP required by applicable requirements of the PCAOB regarding the independent registered public accounting firm’s communications with the Audit Committee concerning independence, and has discussed with the independent registered public accounting firm the firm’s independence. Based on the foregoing, the Audit Committee has recommended to the Board of Directors that the audited financial statements be included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2024.

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This Report of the Audit Committee of the Board of Directors is not “soliciting material,” shall not be deemed “filed” with the SEC and shall not be incorporated by reference by any general statement incorporating by reference this proxy statement into any filing under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, whether made before or after the date hereof and irrespective of any general incorporation language in any such filing, except to the extent that the Company specifically incorporates this information by reference, and shall not otherwise be deemed filed under such acts.

The foregoing report has been furnished by the Audit Committee.

Compensation Committee

Our Compensation Committee currently consists of Annie Drapeau (Chairperson), John Furey, Peter Hirth and Heath Lukatch. Dr. Hirth, whose term will end at the Annual Meeting, will remain a member of our Compensation Committee until the Annual Meeting. Our Board of Directors has determined that each member of the Compensation Committee is independent under the listing standards of Nasdaq and a “non-employee director” as defined in Rule 16b-3 promulgated under the Exchange Act.

The primary purpose of our Compensation Committee is to discharge the responsibilities of our Board of Directors in overseeing our compensation policies, plans and programs and to review and determine the compensation to be paid to our executive officers, directors and other senior management, as appropriate. Specific responsibilities of our Compensation Committee include:

Compensation Committee Interlocks and Insider Participation

None of the members of the Compensation Committee is currently or has been at any time one of our officers or employees. None of our executive officers currently serves, or has served during the last year, as a member of the board of directors or compensation committee of any entity that has one or more executive officers serving as a member of our Board of Directors or Compensation Committee.

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Report of the Compensation Committee of the Board of Directors

The Compensation Committee has reviewed and discussed the section of this proxy statement titled “Compensation Discussion and Analysis” with management. Based on such review and discussion, the Compensation Committee has recommended to the Board of Directors that the section titled “Compensation Discussion and Analysis” be included in this proxy statement and incorporated into our Annual Report on Form 10-K for the fiscal year ended December 31, 2024.

This Report of the Compensation Committee of the Board of Directors is not “soliciting material,” shall not be deemed “filed” with the SEC and shall not be incorporated by reference by any general statement incorporating by reference this proxy statement into any filing under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, whether made before or after the date hereof and irrespective of any general incorporation language in any such filing, except to the extent that the Company specifically incorporates this information by reference, and shall not otherwise be deemed filed under such acts.

The foregoing report has been furnished by the Compensation Committee.

Nominating and Corporate Governance Committee

Our Nominating and Corporate Governance Committee consists of Halley Gilbert (Chairperson), Annie Drapeau and Peter Hirth. Dr. Hirth, whose term will end at the Annual Meeting, will remain a member of our Nominating and Corporate Governance Committee until the Annual Meeting. Our Board of Directors has determined that each member of the Nominating and Corporate Governance Committee is independent under the applicable Nasdaq listing standards.

Specific responsibilities of our Nominating and Corporate Governance Committee include:

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Director Nomination Process

Director Qualifications

Our Nominating and Corporate Governance Committee is responsible for reviewing with our Board of Directors, on an annual basis, the appropriate characteristics, skills and experience required for the Board of Directors as a whole and for its individual members. In evaluating the suitability of individual candidates (both new candidates and current members), the Board of Directors will take into account many factors, including the following:

The Nominating and Corporate Governance Committee also will consider such factors as the ability to offer advice and guidance to management, having sufficient time to devote to the affairs of the Company, demonstrated excellence in his or her field, the ability to exercise sound business judgment and the commitment to rigorously represent the long-term interests of our stockholders. However, the Nominating and Corporate Governance Committee retains the right to modify these qualifications from time to time. Candidates for director nominees are reviewed in the context of the current composition of the Board of Directors and the long-term interests of stockholders. In conducting this assessment, the Nominating and Corporate Governance Committee typically considers such other factors as it deems appropriate, given the current needs of the Board of Directors and Vaxcyte, to maintain a balance of knowledge, experience and capability.

Identification and Evaluation of Nominees for Director

The Nominating and Corporate Governance Committee identifies nominees for director by first evaluating for re-nomination the current members of our Board of Directors whose terms of office are set to expire and are willing to continue in service.

In the case of potential nominees, the Nominating and Corporate Governance Committee uses its network of contacts to compile a list of potential candidates, but may also engage, if it deems appropriate, a professional search firm. The Nominating and Corporate Governance Committee conducts any appropriate and necessary inquiries into the backgrounds and qualifications of possible candidates after considering the function and needs of the Board of Directors. The Nominating and Corporate Governance Committee interviews potential nominees and meets to discuss and consider the candidates’ qualifications and then selects a nominee for recommendation to the Board of Directors by majority vote.

In the case of incumbent directors whose terms of office are set to expire, the Nominating and Corporate Governance Committee reviews these directors’ service to Vaxcyte during their terms, including the number of meetings attended, level of participation, quality of performance and any other relationships and transactions that might impair the directors’ independence, as well as the overall composition of the Board of Directors, balancing the value of continuity of service by existing members of our Board of Directors with the value of obtaining new skill sets and expertise.

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DIRECTOR COMPENSATION

Director Compensation for 2024

The following table sets forth information regarding the compensation earned by or paid to our directors during the year ended December 31, 2024, other than Grant E. Pickering, our Chief Executive Officer, who is also a member of our Board of Directors but did not receive any additional compensation for service as a director. The compensation of Mr. Pickering as a named executive officer is set forth below in the subsection titled “Executive Compensation—2024 Summary Compensation Table.”

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Non-Employee Director Compensation

Upon recommendation of the Compensation Committee (in consultation with Pay Governance LLC (“Pay Governance”), its independent compensation consultant), our Board of Directors approved the following compensation for service on our Board of Directors, effective April 1, 2024:

Equity Compensation

Any person who is elected or appointed as a non-employee director for the first time will automatically, upon the date of his or her initial election or appointment, receive a nonstatutory stock option to purchase shares of our common stock with an equivalent value of $800,000 (the “Initial Grant”). The Initial Grant will vest over 36 months, 1/3 of which will vest on the anniversary date on which the non-employee director was appointed to our Board of Directors and 1/36 of which will vest monthly thereafter, subject to the director’s continuous service to us through each such date.

On the date of each annual meeting of stockholders, each non-employee director will receive an equity grant with an equivalent value of $450,000, 75% percent of which will be in the form of a nonstatutory stock option to purchase shares of our common stock (the “Annual Option Grant”) and 25% of which will be in the form of restricted stock units (the “Annual RSU Grant” and together with the Annual Option Grant, the “Annual Grant”). The Annual Option Grant will vest monthly and fully vest on the earlier of the first anniversary of the grant date or the day prior to the next annual meeting of stockholders and the Annual RSU Grant will fully vest on the earlier of the first anniversary of the grant date or the day prior to the next annual meeting of stockholders, subject to the director’s continuous service to us through each such date. Both the Initial Grant and the Annual Grant would become fully vested upon a change in control, subject to the director’s continuous service to us through such date.

Our directors are subject to stock ownership guidelines adopted by our Compensation Committee. A more detailed discussion of our stock ownership guidelines is set forth in the subsection titled “Corporate Governance and Board Matters—Stock Ownership Guidelines.”

Cash Compensation

In addition, each non-employee director is entitled to receive the following cash compensation for services on our Board of Directors and its committees as follows:

The annual cash compensation amounts are payable in equal quarterly installments, in arrears no later than 30 days following the end of each quarter in which the service occurred, prorated for any partial quarter of service.

Expenses

We reimburse each eligible non-employee director for ordinary, necessary and reasonable out-of-pocket travel expenses to cover in-person attendance at and participation in meetings of our Board of Directors and any committee of the Board of Directors.

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PROPOSAL NO. 2

RATIFICATION OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

The Audit Committee of the Board of Directors has selected Deloitte & Touche LLP as our independent registered public accounting firm for the year ending December 31, 2025 and has further directed that management submit the appointment of its independent registered public accounting firm for ratification by the stockholders at the Annual Meeting. Deloitte & Touche LLP has served as the Company’s independent registered public accounting firm since 2017. Representatives of Deloitte & Touche LLP are expected to be present at the Annual Meeting. They will have an opportunity to make a statement if they so desire and will be available to respond to appropriate questions.

Neither our Bylaws nor other governing documents or Delaware law require stockholder ratification of the appointment of Deloitte & Touche LLP as our independent registered public accounting firm. However, the Audit Committee of the Board of Directors is submitting the appointment of Deloitte & Touche LLP to the stockholders for ratification as a matter of good corporate practice. If the stockholders fail to ratify the appointment, the Audit Committee will reconsider whether or not to retain that firm. Even if the appointment is ratified, the Audit Committee in its discretion may direct the appointment of a different independent registered public accounting firm at any time during the year if they determine that such a change would be in the best interests of the Company and its stockholders.

The affirmative vote of the holders of a majority of the shares electronically present online or represented by proxy and entitled to vote on the matter at the Annual Meeting will be required to approve this Proposal No. 2.

OUR BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE RATIFICATION OF DELOITTE & TOUCHE LLP AS OUR INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM.

Principal Accountant Fees and Services

The following table represents aggregate fees billed to us for the years ended December 31, 2024 and 2023 by Deloitte & Touche LLP, our independent registered public accounting firm.

Pre-Approval Procedures

The Audit Committee has procedures in place for the pre-approval of audit and non-audit services rendered by the Company’s independent registered public accounting firm, Deloitte & Touche LLP. The Audit Committee generally pre-approves specified services in the defined categories of audit services, audit-related services and

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tax services up to specified amounts. Pre-approval may also be given as part of the Audit Committee’s approval of the scope of the engagement of the independent registered public accounting firm or on an individual, explicit, case-by-case basis before the independent registered public accounting firm is engaged to provide each service. The pre-approval of services may be delegated to one or more of the Audit Committee’s members, but the decision must be reported to the full Audit Committee at its next scheduled meeting.

The Audit Committee has determined that the rendering of services other than audit services by Deloitte & Touche LLP is compatible with maintaining the independent registered public accounting firm’s independence.

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PROPOSAL NO. 3

APPROVAL, ON A NON-BINDING, ADVISORY BASIS OF THE COMPENSATION OF OUR NAMED EXECUTIVE OFFICERS

In accordance with the requirements of Section 14A of the Exchange Act, we are providing our stockholders the opportunity to vote to approve, on a non-binding, advisory basis, the compensation of our named executive officers (as disclosed under “Executive Compensation—Compensation Discussion and Analysis,” the tables included under the heading “Executive Compensation” and the accompanying narrative). At the 2022 Annual Meeting of Stockholders, our stockholders indicated their preference that the Company solicit a non-binding advisory vote on the compensation of the named executive officers, commonly referred to as a “say-on-pay vote,” every year. The Board of Directors has adopted a policy that is consistent with that preference. In accordance with that policy, this year, the Company is again asking the stockholders to approve, on an advisory basis, the compensation of the Company’s named executive officers as disclosed in this proxy statement in accordance with SEC rules.

You are encouraged to review the section titled “Executive Compensation” and, in particular, the section titled “Executive Compensation—Compensation Discussion and Analysis” in this proxy statement, which provide a comprehensive review of our executive compensation program and its elements, objectives and rationale.

The vote on this resolution is not intended to address any specific element of compensation, rather the vote relates to the compensation of our named executive officers in its totality, as described in this proxy statement in accordance with the compensation disclosure rules of the SEC.

In accordance with Section 14A of the Exchange Act rules, stockholders are asked to approve the following non-binding resolution:

“RESOLVED, that the Company’s stockholders hereby approve, on a non-binding, advisory basis, the compensation of the Company’s named executive officers, as disclosed in the Company’s proxy statement for the 2025 Annual Meeting of Stockholders, pursuant to the compensation disclosure rules of the SEC, including the Compensation Discussion and Analysis, the compensation tables and the accompanying narrative.”

The approval of this non-binding proposal requires the affirmative vote of a majority of the voting power of the shares of our common stock present at the meeting (by virtual attendance) or by proxy and entitled to vote thereon.

Since this proposal is an advisory vote, the result will not be binding on our Board of Directors or our Compensation Committee. However, our Board of Directors values our stockholders’ opinions, and our Board of Directors and the Compensation Committee will take into account the outcome of the advisory vote when considering future executive compensation decisions. Unless the Board of Directors decides to modify its policy regarding the frequency of soliciting say-on-pay advisory votes on the compensation of the Company’s named executive officers, the next scheduled say-on-pay vote will be at the 2026 Annual Meeting of Stockholders.

OUR BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE APPROVAL OF THE NON-BINDING ADVISORY RESOLUTION ON NAMED EXECUTIVE OFFICER COMPENSATION.

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EXECUTIVE OFFICERS

Andrew Guggenhime, M.B.A. Mr. Guggenhime has served as our President since January 2021 and as our Chief Financial Officer since May 2020. Mr. Guggenhime also served as our Chief Business Officer from May 2020 to January 2021. Prior to joining Vaxcyte, Mr. Guggenhime held various roles at Dermira, Inc., a publicly traded biopharmaceutical company, including Chief Operating Officer from April 2014 to May 2018 and Chief Financial Officer from April 2014 to April 2020, following its acquisition by Eli Lilly and Company in February 2020. From September 2011 to April 2014, Mr. Guggenhime served as Chief Financial Officer of CardioDx, Inc., a molecular diagnostics life sciences company, and as a member of the CardioDx board of directors from April 2014 until July 2016. Prior to that, Mr. Guggenhime served as Chief Financial Officer at Calistoga Pharmaceuticals, Inc., a biotechnology company that was acquired by Gilead Sciences, Inc. Mr. Guggenhime also previously served as Senior Vice President and Chief Financial Officer at Facet Biotech Corporation, a biotechnology company, Chief Financial Officer at PDL BioPharma, Inc. a biotechnology company, and Vice President, Corporate Development and then Senior Vice President and Chief Financial Officer at Neoforma, Inc., a provider of supply-chain management solutions for the healthcare industry. Mr. Guggenhime has served as a member of the boards of directors of Sling Therapeutics, a privately held biopharmaceutical company, since June 2024 and of Caribou Biosciences, Inc., a publicly traded biotechnology company, since April 2021, and as chairman of Caribou’s board of directors since July 2021. Mr. Guggenhime previously served as a member of the board of directors of Metacrine, Inc., a publicly traded biopharmaceutical company, from July 2018 to March 2023. Mr. Guggenhime holds a B.A. in International Politics and Economics from Middlebury College and an M.B.A. from the J.L. Kellogg Graduate School of Management at Northwestern University.

Jim Wassil, M.S., M.B.A. Mr. Wassil has served as our Chief Operating Officer since December 2019 and as Executive Vice President since March 2022. From May 2015 to December 2019, Mr. Wassil served as Vice President and Global Health and Value Business Unit Lead, Vaccines at Pfizer Inc., a publicly traded multinational pharmaceutical company. From August 2008 to May 2015, Mr. Wassil served as Head, Global Product Development Meningococcal Vaccines and Head, U.S. Marketing for Meningococcal Vaccines at Novartis AG., a publicly traded multinational pharmaceutical company. From 1992 to 2008, Mr. Wassil held various roles of increasing responsibility with the vaccine division of Merck & Co., Inc., a publicly traded multinational pharmaceutical company, including in research, quality, technology transfer, regulatory and commercial, culminating with his role as Senior Director, International Marketing, Pediatric Vaccines. Mr. Wassil previously served as a member of the board of directors of Icosavax, Inc., a publicly traded biopharmaceutical company, from June 2022 to February 2024 when it was acquired by AstraZeneca. Mr. Wassil is a member of the Infectious Diseases Society of America. Mr. Wassil holds a B.S. in Chemistry/Biology from the University of Notre Dame and a M.S. in Bioorganic Chemistry and an M.B.A. from Lehigh University.

Mikhail Eydelman, J.D. Mr. Eydelman has served as our Senior Vice President, General Counsel and Corporate Secretary since April 2022, as well as our Chief Compliance Officer since March 2023. From 2017 to April 2022, Mr. Eydelman served as General Counsel and Board Secretary at Sagent Pharmaceuticals, Inc., a U.S. subsidiary of a publicly traded Japanese pharmaceutical company. From 2016 to 2017, Mr. Eydelman

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served as Assistant General Counsel at Integrated DNA Technologies, a privately held supplier of custom nucleic acids, which was acquired by Danaher Corporation. From 2012 to 2016, Mr. Eydelman served in roles of increasing responsibility at Akorn, Inc., a publicly traded specialty pharmaceutical company. Mr. Eydelman has also served as an attorney at the law firms Latham & Watkins, Allen & Overy and Bryan Cave. Mr. Eydelman holds a B.A. in Economics from Brandeis University and a J.D. from New York University School of Law.

Our executive officers are elected by our Board of Directors and serve at the discretion of our Board of Directors until their successors have been duly elected and qualified or until their earlier resignation or removal.

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EXECUTIVE COMPENSATION

Compensation Discussion and Analysis

Overview

This Compensation Discussion and Analysis section discusses our executive compensation policies and how and why our Compensation Committee arrived at specific compensation decisions for the year ended December 31, 2024 for the individuals who served as our PEO and PFO and our two other most highly compensated executive officers as of December 31, 2024, collectively referred to as our “named executive officers.” During 2024, we only had four executive officers. Accordingly, our group of named executive officers for 2024 is limited to the following four individuals:

Executive Summary

2024 was a defining year for Vaxcyte, marked by meaningful progress across our pneumococcal conjugate vaccine (“PCV”) franchise in the pediatric and adult populations, including positive topline data from the adult Phase 1/2 study of VAX-31, our 31-valent PCV candidate, completing enrollment for our infant Phase 2 study of VAX-24, our 24-valent PCV candidate, initiating our infant Phase 2 study of VAX-31, advancing several manufacturing initiatives, and further strengthening our financial position following the completion of two follow-on equity offerings and sales made under our Amended Open Market Sales Agreement^SM with Jefferies LLC (the “ATM Facility”) that in aggregate generated approximately $2.6 billion in gross proceeds.

We once again delivered strong results and continued to advance our strategic goals in 2024. Some of the key results as of December 31, 2024 include:

Stockholder Returns Have Exceeded Benchmarks:

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PCV Franchise Adult Indication:

In the Phase 1/2 study, VAX-31 was observed to be well tolerated and demonstrated a safety profile at all doses studied through the full six-month evaluation period similar to Prevnar 20^® (“PCV20”). VAX-31 showed robust opsonophagocytic activity (“OPA”) immune responses for all 31 serotypes at all doses studied. For all 11 incremental serotypes unique to VAX-31, and not in PCV20, all three doses met the superiority criteria. At the middle and high doses, VAX-31 met or exceeded the OPA response non-inferiority criteria for all 20 serotypes common with PCV20. At the VAX-31 high dose, average OPA immune responses were greater for 18 of 20 serotypes compared to PCV20 (geometric mean ratio (“GMR”) greater than 1.0), with seven of these serotypes achieving statistically higher immune responses compared to PCV20. At the middle dose, 13 of 20 serotypes had a GMR greater than 1.0 and five serotypes achieved statistically higher immune responses compared to PCV20.

PCV Franchise Infant Indication:

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Capital Raising:

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Continued Execution and Achievement of Corporate Goals

As reflected throughout this section, we achieved all of our base corporate goals at or above the target level of performance, and numerous other accomplishments in 2024, marking another strong year for Vaxcyte.

In February 2025, the Compensation Committee recommended, and the Board of Directors approved, an annual bonus payout of 150% of target for each of our named executive officers. A more detailed discussion of our annual bonus program is set forth below in the subsections titled “2024 Executive Compensation Program—Executive Bonus Goal Setting” and “2024 Executive Compensation Program—Fiscal Year 2024 Bonus Payouts.”

In November 2024, the Compensation Committee, in consultation with Pay Governance and with unanimous support of the full Board of Directors, determined that it would be appropriate and in the best interests of the Company and our stockholders to grant a special equity-based incentive award to all employees, with grants to employees at the vice president level and above being performance-based (the “Special Outperformance and Recognition Award”). The Special Outperformance and Recognition Award reflects both the Board of Directors’ recognition of the Company’s significant achievements in 2024 as described above and, more importantly, our commitment to drive superior long-term performance and stockholder value creation. The Special Outperformance and Recognition Award establishes exceptionally high-performance thresholds designed to aggressively align executive incentives with stockholder interests while further motivating executives to sustain outstanding performance and results over the long term.

The Special Outperformance and Recognition Award consists of performance-contingent stock options (“PCSOs”) and performance restricted stock units (“PSUs”), both of which will only deliver value to the recipients if the Company delivers significant value to stockholders.

The PCSOs, which account for 50% of the intended target grant value, have a 10-year term and vest in one-third increments on the third, fourth, and fifth anniversaries of the grant date, subject to continued service through the applicable vesting date. Critically, these options cannot be exercised until the Company’s closing stock price average over a one-year period is at least $154.05 (150% of the grant date closing price)—an ambitious hurdle intended to drive meaningful share price appreciation. For context, the last reported sale price of our Common Stock on the Nasdaq Global Select Market on April 17, 2025 was $30.65 per share, therefore, in order for any PCSOs to become exercisable, the closing stock price of our Common Stock would need to increase over 500% and, on average, maintain that increased stock price for one year.

The PSUs, representing the remaining 50% of the intended target grant value, are contingent upon meeting increasingly stringent performance thresholds. Vesting is directly linked to the Company’s relative TSR over a four-year period against a peer group constituting the Nasdaq Biotechnology Index. Depending on performance, the number of shares delivered can range from 0% to 250% of the target amount, subject to continued employment through the vesting date. Importantly, no shares will vest unless the Company’s TSR reaches at least the 60^th percentile, at which point 50% of the shares vest, and at the highest level would require a relative TSR of at least the 95^th percentile. For context, the beginning stock price that will be used to calculate the Company’s TSR is $102.70 (the grant date closing price on November 7, 2024). By establishing challenging performance targets with corresponding incentives, the Board of Directors has introduced an additional motivational framework designed to drive superior results.

By embedding these stringent and highly demanding performance thresholds into the Special Outperformance and Recognition Awards, the Board of Directors seeks to continue fostering a culture of excellence and a deep alignment between employees and stockholders. Through the Special Outperformance and Recognition Award,

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leadership is both rewarded for its 2024 successes and challenged to continue delivering substantial, market-beating performance that will benefit all stakeholders over the long term. Only by exceeding these highly rigorous goals can recipients fully benefit—ensuring alignment between leadership and stockholders.

A more detailed discussion of the Special Outperformance and Recognition Award is set forth below in the subsection titled “2024 Executive Compensation Program—Special Outperformance and Recognition Award.

Pipeline Overview

Our pipeline includes:

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Executive Compensation Overview

The important features of our executive compensation program include the following:

Objectives, Philosophy and Elements of Executive Compensation

Our compensation program aims to achieve the following main objectives:

Our executive compensation program generally consists of the following three principal components: base salary, performance-based bonus and long-term equity incentive compensation. We also provide our executive officers with the same benefits available to all our employees, including retirement benefits under our defined

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contribution employee retirement plan (“401(k) plan”) and participation in employee benefit plans. The below chart summarizes the three main elements of our executive compensation, their objectives and key features.

We aim to provide a competitive compensation package to our executive officers that balances short- and long-term incentives to drive the achievement of measurable corporate objectives. We believe that this approach fosters an alignment between executive interests, stockholder value and corporate success.

We do not have any formal policies for allocating salary, performance bonus awards and equity grants, or the balance between short and long-term compensation. Instead, the Compensation Committee exercises its discretion to determine a total compensation mix for each named executive officer. However, we have

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historically structured a significant portion of our named executive officers’ total target compensation around performance-based bonus opportunities and long-term equity awards. This aligns the executive officers’ incentives with both the interests of our corporate goals and stockholder interests.

How We Determine Executive Compensation

Role of our Compensation Committee, Management and the Board of Directors

The Compensation Committee is appointed by our Board of Directors and helps our Board of Directors oversee our compensation policies, plans and programs with the goal of attracting, incentivizing, retaining and rewarding top- quality executive management and employees. The Compensation Committee is responsible for reviewing and determining all compensation paid to our executive officers, including our named executive officers, and also reviewing our compensation practices and policies as they relate to risk management and risk-taking incentives. Our Compensation Committee consists solely of independent members of the Board of Directors.

The Compensation Committee meets periodically throughout the year to manage and evaluate our executive compensation program, and generally determines the principal components of compensation (base salary, performance bonus and equity awards) for our executive officers on an annual basis; however, decisions may occur at other times for new hires, promotions or other special circumstances as our Compensation Committee determines appropriate. The Compensation Committee does not delegate authority to approve executive officer compensation. From time to time, the Compensation Committee will recommend approval of compensation matters to the Board of Directors, consistent with the Compensation Committee’s charter.

In fulfilling its responsibilities, the Compensation Committee considers input from an independent compensation consultant and, as appropriate, management. Our Chief Executive Officer evaluates and provides to the Compensation Committee performance assessments and compensation recommendations. While our Chief Executive Officer discusses his recommendations with the Compensation Committee, he does not participate in the deliberations concerning, or the determination of, his own performance and compensation. The Compensation Committee discusses and makes final determinations with respect to executive compensation matters without our Chief Executive Officer present during discussions of our Chief Executive Officer’s compensation. From time to time, various other members of management and other employees as well as outside advisors or consultants may be invited by the Compensation Committee to make presentations, provide financial or other background information or advice or otherwise participate in the Compensation Committee meetings.

Role of Compensation Consultant

The Compensation Committee has the sole authority to retain compensation consultants to assist in its evaluation of executive compensation, including the authority to approve the consultant’s reasonable fees and other retention terms. The Compensation Committee retained Pay Governance as its independent compensation consultant for 2024.

Pay Governance’s engagement included:

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The Compensation Committee has analyzed whether the work of Pay Governance as compensation consultant raises any conflict of interest, taking into account relevant factors in accordance with SEC guidelines (the “Independence Assessment”). Based on its analysis, the Compensation Committee determined that the work of Pay Governance and the individual compensation advisors employed by Pay Governance does not create any conflict of interest pursuant to the SEC rules and stock exchange listing standards.

Use of Competitive Market Compensation Data

The Compensation Committee believes that it is important when making its compensation decisions to be informed as to the current practices of comparable public companies with which we compete for top talent. To this end, the Compensation Committee directed Pay Governance to develop a proposed peer group list of the publicly traded companies to be used in connection with assessing our compensation practices.

Pay Governance proposed, and the Compensation Committee approved, a group of public companies that are reasonably comparable to Vaxcyte in terms of industry and financial characteristics to provide management and the Compensation Committee with relevant compensation information to support compensation decision-making. The executive compensation peer group was intended to reflect companies with executive positions of similar scope and complexity to Vaxcyte. In determining the peer group, Pay Governance considered Vaxcyte’s recent growth and performance with an understanding that there is a limited universe of clinical stage companies with a similar valuation and generally screened for companies that (i) were mid- to late-stage clinical companies and recently commercial companies operating within the GICS Industry Pharmaceutical and Biotechnology; (ii) had a market capitalization multiple of approximately 0.3x to 3.0x of Vaxcyte and a headcount generally above 100 employees; (iii) had a similar scientific focus and complexity of manufacturing/operations; and (iv) went public after 2010 but before 2023.

Pay Governance also considered several secondary factors, including recent share price performance and other financial metrics. The peer group with respect to 2024 was as follows:

The Compensation Committee reviews our peer group at least annually and makes adjustments to its composition, if warranted, taking into account changes in both our business and the businesses of the companies in the peer group. Our updated peer group for 2024 reflects our advancement into late-stage clinical trials for our PCV franchise, our increased market cap, our growing headcount and our complex manufacturing needs. This has resulted in a number of changes to the composition of the peer group, which the Compensation Committee determined to be appropriate given the evolution of our business over time.

Using data compiled from the peer companies, Pay Governance completed an assessment of our executive compensation to inform the Compensation Committee’s determinations regarding executive compensation for 2024. Pay Governance prepared, and the Compensation Committee reviewed, a range of market data reference points (generally at the 25^th, 50^th and 75^th percentiles of the market data) with respect to base salary, performance bonuses, total target cash compensation, equity compensation and total direct compensation with respect to each of the named executive officers. The Compensation Committee generally considered equity levels between the 50^th and 75^th percentile of the market data and reviewed these market data reference points as a helpful reference point in making 2024 compensation decisions, while making allowances for different roles and circumstances. The Compensation Committee generally did not strictly target a specific percentile in making 2024 compensation

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decisions. Market data is only one of the factors that the Compensation Committee considers in making compensation decisions. The Compensation Committee considers other factors as described below under “Factors Used in Determining Executive Compensation.”

Factors Used in Determining Executive Compensation

The Compensation Committee sets the compensation of our named executive officers at levels determined to be competitive and appropriate for each named executive officer, using their professional experience and judgment. Pay decisions are not made by use of a formulaic approach or benchmark; the Compensation Committee believes that executive pay decisions require consideration of a multitude of relevant factors which may vary from year to year. In making executive compensation decisions, the Compensation Committee generally takes into consideration the factors listed below.

“Say-on-Pay” Vote

In June 2024, we held a stockholder advisory vote on the compensation of our named executive officers. Our stockholders approved, on an advisory basis, the compensation of our named executive officers, with 92% of stockholder votes cast in favor of our “say-on-pay” resolution. In evaluating our compensation practices during fiscal 2024 and in early 2025, we were mindful of the support our stockholders expressed for our compensation philosophy. As a result, the Compensation Committee will continue to reinforce a pay-for-performance philosophy that ensures a direct link between stockholder interests and the interests of our executive officers. The Compensation Committee will continue to consider stockholder concerns and feedback in the future.

2024 Executive Compensation Program

Base Salary

Base salary represents the fixed portion of the compensation of our executive officers and is an important element of compensation intended to attract and retain highly talented individuals. In February 2024, the Compensation Committee reviewed the base salaries of our executive officers, taking into consideration the competitive market analysis prepared by Pay Governance and the recommendations of our Chief Executive Officer for the other executive officers, as well as the other factors described in the section above. Following this review, the Compensation Committee approved base salary increases for our executive officers and recommended to the Board of Directors a base salary increase for our Chief Executive Officer, to bring their base salaries to levels that were more aligned to the range of those of similarly situated executives at the companies in our peer group.

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The Board of Directors approved the base salary increase for our Chief Executive Officer in February 2024. The base salaries approved for all of our named executive officers, effective as of January 1, 2024, were as follows:

Annual Performance-Based Bonus

Our annual performance-based bonus awards provide incentive compensation (generally paid in cash) that is specifically designed to motivate our executive officers to achieve pre-established, company-wide priorities set by the Compensation Committee and the Board of Directors and to reward them for results and achievements in a given year. The annual target bonus opportunities for our named executive officers are generally determined by the Compensation Committee in the first quarter of each year and expressed as a percentage of each individual’s annual base salary comprising the named executive officer’s potential bonus opportunity. In February 2023, our Board of Directors approved, upon recommendation from our Compensation Committee, the ability of our officers at the level of vice president and above, at their own election, to receive their respective annual performance-based bonus awards in cash or fully vested restricted stock units (“RSUs”). The Board determined that should an officer elect to receive RSUs in lieu of cash, such grant would be issued on the same day as the payment of the cash bonus to all other employees, and the value of such grant would be with respect to a number of shares of our common stock with a fair market value equivalent to the cash value of the bonus at the time it was determined. The number of RSUs granted to such officer is obtained by dividing the cash value of the bonus by the closing price of our common stock on the grant date. Mr. Wassil was the only named executive officer who elected to receive his 2024 bonus in such form, and was granted 5,649 fully vested RSUs using the closing price of our common stock on the grant date of February 28, 2025. The target bonus opportunities approved for, and amounts earned by, our named executive officers for 2024 were as follows:

Executive Bonus Goal Setting

The targets against which performance is measured are generated through our annual budget and strategic planning process. The Board of Directors approved the performance metrics for 2024 performance-based bonus awards in the first quarter of fiscal year 2024, which included a stipulation that the maximum payout for achievement of the corporate goals would be 150%.

The corporate goals for 2024 on which our named executive officer performance bonuses were based included base corporate goals (total weighting of 100%) relating to the achievement of: (i) objectives in support of our VAX-31 adult program, including the completion of the Phase 1/2 study evaluating VAX-31 in healthy adults aged 50 years and older, reporting results from such study, and completion of certain CMC and clinical readiness activities; (ii) objectives in support of our PCV infant programs, including the completion of enrollment for the Phase 2 study evaluating VAX-24 for the prevention of IPD in healthy infants, and certain activities to enable the initiation of the Phase 2 study evaluating VAX-31 in healthy infants in early 2025; (iii) completion of certain buildout objectives for our dedicated manufacturing suite at Lonza intended to support the potential global commercialization of our PCV programs; (iv) objectives in support of VAX-A1 Phase 1/2 development;

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(v) objectives in support of the development of other pipeline programs; (vi) financial objectives, including certain financing and capital raising goals; and (vi) corporate objectives, including management of operating and capital expenses within the annual budget, achievement of a pre-established hiring target, and expansion of our headquarters to accommodate our growing workforce.

The 2024 corporate goals also included stretch goals (total weighting of 50%, and together with the base goals, a total weighting of 150%) relating to the achievement of the following objectives: (i) receipt of positive data from the VAX-31 Phase 1/2 study in adults aged 50 and older; (ii) completion of certain objectives for our dedicated manufacturing suite at Lonza intended to support the potential global commercialization of our PCV programs; (iii) financial objectives, including certain financing and capital raising goals; (iv) certain objectives related to our Phase 2 study evaluating VAX-24 for the prevention of IPD in healthy infants; and (v) certain CMC-related objectives.

In February 2025, the Board of Directors, on the recommendation of the Compensation Committee, certified the achievement of our corporate performance goals at a weighting of 150%.

Fiscal Year 2024 Bonus Payouts

The Compensation Committee and Board of Directors considered the immense progress made on the objectives, with specific emphases on the positive results from the VAX-31 Phase 1/2 study in healthy adults aged 50 years and older, completion of two successful follow-on financings with gross proceeds of approximately $2.4 billion, the Company’s success in executing on the VAX-24 and VAX-31 infant clinical trials, including initiating the VAX-31 infant study ahead of schedule in the fourth quarter of 2024, and preparations for the potential future commercial launch of its PCV franchise programs. Based on the 2024 corporate goals, the Compensation Committee and Board of Directors determined that 25% of the stretch goals (which stretch goals have a total weighting of 50%) were achieved in 2024, and further determined that the remaining 25% would be deemed to have been achieved based on the Compensation Committee’s recognition that (i) certain events which could have resulted in the achievement of the other stretch goals were purposefully deferred for sound strategic reasons and (ii) significant overperformance was achieved with respect to other 2024 goals (e.g., the positive results from the VAX-31 Phase 1/2 study and the successful completion of the follow-on financing in September 2024 that resulted in aggregate gross proceeds to the Company of approximately $1.5 billion). In light of these circumstances, in February 2025, the Compensation Committee recommended, and the Board of Directors approved, a bonus payout of 150% of target for each of our named executive officers.

Equity Awards

We view long-term incentive compensation in the form of equity awards as a critical element of our executive compensation program. The realized value of these equity awards bears a direct relationship to our stock price, and, therefore, these awards are an incentive for our executive officers to create value for our stockholders. Equity awards also help us retain qualified executive officers in a competitive market.

Long-term incentive compensation opportunities in the form of equity awards are granted to our Chief Executive Officer and our other executive officers by the Compensation Committee, and occasionally the Board of Directors upon recommendation from the Compensation Committee. As with other elements of compensation, the Compensation Committee determines the amount of long-term incentive compensation for our executive officers as part of its annual compensation review and after taking into consideration the individual officer’s responsibilities and performance and existing equity retention profiles, our total annual projected equity budget and the other factors described in “Factors Used in Determining Executive Compensation” above. For awards to executive officers other than our Chief Executive Officer, the Compensation Committee also takes into account the recommendations of our Chief Executive Officer with respect to appropriate grants and any particular individual circumstances. The amounts of the equity awards are intended to provide competitively sized awards and resulting target total direct compensation opportunities that the Compensation Committee believes are reasonable and appropriate taking into consideration the factors described herein.

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2024 Annual Equity Awards

In February 2024, the Compensation Committee approved the following annual equity grants (the “Annual Equity Grant”) for our named executive officers (except that Mr. Pickering’s Annual Equity Grant was approved by the Board of Directors), which were granted in February 2024. The stock options vest monthly over a four-year period and have an exercise price of $73.82 per share, and 1/4 of the stock awards vested six months from the grant date, and additional 1/8 increments vest semi-annually thereafter.

Special Outperformance and Recognition Awards

In November 2024, the Compensation Committee, in consultation with Pay Governance, and with unanimous support of the full Board of Directors, determined that it would be appropriate and in the best interests of the Company to grant the Special Outperformance and Recognition Awards to our named executive officers, as well as other executives. The Special Outperformance and Recognition Award reflects both the Board of Directors’ recognition of the Company’s significant achievements in 2024 as described above and, more importantly, its commitment to drive superior long-term performance and stockholder value creation. The Special Outperformance and Recognition Award imposes exceptionally high performance thresholds designed to aggressively align executive incentives with stockholder interests and further motivate these individuals to continued delivery of outstanding results over the long term.

The performance-based equity awards included in the Special Outperformance and Recognition Award included performance-contingent stock options (“PCSOs”) and performance restricted stock units (“PSUs”). The total Special Outperformance and Recognition Award grant date values awarded to our named executive officers were approximately as follows: (i) $25,000,000 to Mr. Pickering, (ii) $11,000,000 to each of Messrs. Guggenhime and Wassil, and (iii) $1,700,000 to Mr. Eydelman. The table below sets forth the portions of the Special Outperformance and Recognition Award which were granted to our named executive officers in the forms of PCSOs and PSUs:

Additional discussion of the Special Outperformance and Recognition Award is set forth above in the subsection titled “Compensation Discussion and Analysis—Executive Summary—Continued Execution and Achievement of Corporate Goals.”

Performance Conditions of PCSOs

The PCSOs are subject to (i) a service-based vesting condition (vesting as to one-third of the shares on each of the third, fourth and fifth anniversaries of the date of grant, subject to continued employment through the

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applicable vesting date) and (ii) a performance-based vesting condition (which generally requires that the closing price of our Common Stock average, over a one-year period, is at least $154.05—which represents 150% of the grant date closing price).

Performance Conditions of PSUs

In general, the PSUs are subject to a performance-based vesting condition. The PSUs are eligible to vest based on relative TSR as measured against a peer group of companies that comprise the Nasdaq Biotechnology Index as of the grant date over a four-year performance period, subject to continued employment through the vesting date. The percentile ranks and corresponding payout percentages (number of shares of our Common Stock as a percent of target) are as follows:

Employment, Severance and Change in Control Arrangements

Employment Agreements

We have entered into employment agreements or offer letters with each of our named executive officers. We designed these agreements to be part of a competitive compensation package and to keep our named executive officers focused on our business goals and objectives. These agreements or offer letters provide for base salaries and incentive compensation, and each component reflects the scope of each named executive officer’s anticipated responsibilities and the individual experience they bring to the Company. Each named executive officer is also eligible to participate in our employee benefit plans on the same terms as other regular, full-time employees. In addition, each of our named executive officers has executed our standard proprietary information and invention assignment agreement. The key terms of the offer letters or employment agreements are described below.

Grant E. Pickering

We entered into an employment agreement with Mr. Pickering, our Chief Executive Officer, dated January 21, 2016, which sets forth the initial terms and conditions of his employment with us. Mr. Pickering’s employment is at will and may be terminated at any time, with or without cause.

Andrew Guggenhime

We entered into an offer letter with Mr. Guggenhime, our President and Chief Financial Officer on April 17, 2020, which sets forth the initial terms and conditions of his employment with us. Mr. Guggenhime’s employment is at will and may be terminated at any time, with or without cause.

Jim Wassil

We entered into an offer letter with Mr. Wassil, our Executive Vice President and Chief Operating Officer, dated November 15, 2019, which sets forth the initial terms and conditions of his employment with us. Mr. Wassil’s employment is at will and may be terminated at any time, with or without cause.

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Mikhail Eydelman

We entered into an offer letter with Mr. Eydelman, our Senior Vice President, General Counsel, Chief Compliance Officer and Corporate Secretary, dated March 4, 2022, which sets forth the initial terms and conditions of his employment with us. Mr. Eydelman’s employment is at will and may be terminated at any time, with or without cause.

Executive Change in Control and Severance Agreements

We have entered into Executive Change in Control and Severance Agreements with each of our named executive officers. The agreements provide for severance benefits upon a termination of employment by the Company without “cause” or by the executive for “good reason,” each as defined in the agreements, each of which we refer to as a qualifying termination. The severance benefits vary depending on whether the qualifying termination occurs during the period three months prior to and 12 months after a “change in control,” as defined in the agreements, which we refer to as the change in control period, or at a time other than during the change in control period.

In the event of a qualifying termination other than during the change in control period, the executive will receive a lump sum severance payment equal to the sum of (i) a number of months of base salary (12 months in the case of Mr. Pickering, nine months in the case of Messrs. Guggenhime, Wassil and Eydelman), (ii) a pro rata target bonus for the year of termination, and (iii) any bonus earned but not yet paid with respect to the year preceding the qualifying termination. The executive will also receive payment of COBRA premiums for the number of months in the severance period. Receipt of severance benefits is contingent upon the executive entering into a release of claims and allowing it to become effective.

In the event of a qualifying termination during the change in control period, the executive will receive a lump sum severance payment equal to the sum of (i) a number of months of base salary (18 months in the case of Mr. Pickering, 12 months in the case of Messrs. Guggenhime, Wassil and Eydelman), (ii) a multiple of the executive’s target bonus for the year of termination (150% in the case of Mr. Pickering, 100% in the case of Messrs. Guggenhime, Wassil and Eydelman) and (iii) any bonus earned but not yet paid with respect to the year preceding the qualifying termination. The executive will also receive payment of COBRA premiums for the number of months in the severance period and full vesting of all time-based equity awards. The vesting of performance-based equity awards will be based on the provisions of such awards. Receipt of severance benefits is contingent upon the executive entering into a release of claims and allowing it to become effective.

Other Elements of Compensation

Health, Welfare and Retirement Benefits

Our named executive officers are eligible to participate in all of our employee benefit plans, such as medical, dental, vision, group life, short and long-term disability plans, in each case on the same basis as other employees, subject to applicable laws.

401(k) Plan

We maintain a 401(k) plan that provides eligible U.S. employees with an opportunity to save for retirement on a tax advantaged basis. Eligible employees are able to defer eligible compensation up to certain Code limits, which are updated annually. We have the ability to make matching and discretionary safe harbor contributions to the 401(k) plan. Beginning January 1, 2022, an employee who contributes 5% of compensation or more will receive a matching contribution equal to 4% of compensation, subject to the maximum annual employer contribution limit. The 401(k) plan is intended to be qualified under Section 401(a) of the Code, with the related trust intended to be tax exempt under Section 501(a) of the Code. As a tax-qualified retirement plan, contributions to the 401(k) plan are deductible by us when made, and contributions and earnings on those amounts are not generally taxable to the employees until withdrawn or distributed from the 401(k) plan.

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Work Anniversary Gift

In July 2023, we implemented a Work Anniversary Program, which is an employee recognition program to celebrate and acknowledge years worked at Vaxcyte by all full-time employees. Upon reaching an anniversary milestone of one year, three years, five years and ten years, full time employees receive an associated award of a $50 gift card, $250 gift card, $500 cash award or $1,000 cash award, respectively (“Anniversary Award”).

Perquisites and Other Personal Benefits

We do not provide perquisites or other personal benefits to our named executive officers.

No Tax Gross-Ups

In 2024, we did not make gross-up payments to cover our named executive officers’ personal income taxes that pertained to any of the compensation or benefits paid or provided by the Company and no named executive officer is party to an agreement providing for a gross-up payment.

Clawbacks

Effective October 2, 2023, our Compensation Committee adopted an incentive compensation recoupment policy (“Clawback Policy”) as required by Rule 10D-1 under the Exchange Act and the corresponding Nasdaq listing standards. In the event the Company is required to prepare an accounting restatement to correct material noncompliance with any financial reporting requirement under U.S. federal securities laws, the Clawback Policy generally requires the Company to recover erroneously awarded compensation that is granted, earned or vested based in whole or in part upon the attainment of a financial reporting measure and that is received by our current and former executive officers (as defined in Rule 10D-1) during the three fiscal years preceding the date that the Company is required to prepare the accounting restatement. The amount recoverable is the compensation paid or payable in excess of the amount that would have been paid or payable based on the restated financial results. The Compensation Committee administers the Clawback Policy.

In addition, as a public company, if we are required to restate our financial results due to our material noncompliance with any financial reporting requirements under the federal securities laws as a result of misconduct, our Chief Executive Officer and Chief Financial Officer may be legally required to reimburse the Company for any bonus or other incentive-based or equity-based compensation they receive in accordance with the provisions of section 304 of the Sarbanes-Oxley Act of 2002.

Policy Prohibiting Hedging and Pledging

Our Insider Trading Policy prohibits all directors, officers, other employees and designated consultants from purchasing our stock on margin or holding our stock in a margin account, pledging our stock as collateral or engaging in hedging, derivative or similar transactions with respect to our stock, such as prepaid variable forwards, equity swaps, collars, exchange funds, puts, calls and short sales. Certain exceptions to this policy may be approved by our General Counsel or Chief Compliance Officer so long as such exceptions are compliant with applicable laws and regulations.

Stock Ownership Guidelines

Our named executive officers are subject to stock ownership guidelines adopted by our Compensation Committee. A more detailed discussion of our stock ownership guidelines is set forth in the subsection titled “Corporate Governance and Board Matters—Stock Ownership Guidelines.”

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Tax and Accounting Implications

Under ASC Topic 718, we are required to estimate and record an expense for each award of equity compensation over the vesting period of the award. We record share-based compensation expense on an ongoing basis according to ASC Topic 718.

Under Section 162(m) of the Internal Revenue Code (“Section 162(m)”), compensation paid to each of our “covered employees” that exceeds $1 million per taxable year is generally non-deductible. Although the Compensation Committee will continue to consider tax implications as one factor in determining executive compensation, the Compensation Committee also looks at other factors in making its decisions and retains the flexibility to provide compensation for the our named executive officers in a manner consistent with the goals of our executive compensation program and the best interests of the Company and its stockholders, which may include providing for compensation that is not deductible due to the deduction limit under Section 162(m).

Executive Compensation Tables

2024 Summary Compensation Table

The following table presents all of the compensation awarded to, earned by or paid to our named executive officers during the fiscal year ended December 31, 2024. For context, the amounts listed in the “Stock Awards” and “Stock Option Awards” columns are accounting values and do not reflect the actual economic value that may be realized by the named executive officers in connection with such equity awards.

44

45

46

Grants of Plan-Based Awards

The following table presents information regarding each plan-based award granted to our named executive officers during the fiscal year ended December 31, 2024.

47

48

Outstanding Equity Awards as of December 31, 2024

The following table sets forth certain information regarding outstanding equity awards granted to our named executive officers that remain outstanding as of December 31, 2024.