UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 14A

Proxy Statement Pursuant to Section 14(a) of the

Securities Exchange Act of 1934

Filed by the Registrant  ⌧                               Filed by a Party other than the Registrant  ☐

Check the appropriate box:

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BLUEPRINT MEDICINES CORPORATION

(Name of Registrant as Specified In Its Charter)

(Name of Person(s) Filing Proxy Statement, if Other Than the Registrant)

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Payment of Filing Fee (Check all boxes that apply):

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Dear Stockholders,

2024 was a remarkable year of achievement for Blueprint Medicines in our continued effort to drive growth and innovation with operational excellence.   

Last year, we significantly advanced the launch of AYVAKIT^®/AYVAKYT^® (avapritinib), as we brought this important medicine to many more patients with systemic mastocytosis (SM) and achieved global net product revenues of $479 million, representing approximately 135 percent year-over-year growth. Today, AYVAKIT is one of the most successful rare disease launches to date, supported by a compelling benefit-risk profile and our proven commercial capability. AYVAKIT is now approved and reimbursed for at least one indication in 16 countries, with plans for additional country launches in indolent SM (ISM). In 2025, we expect to drive further AYVAKIT growth, with product revenue guidance of $680-$710 million, on path to achieve our goal of $2 billion in revenue by 2030.  

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The SM opportunity is larger than we first thought, and growing faster than we expected.  

As the first therapy approved to treat ISM, AYVAKIT is proving to be a catalyst for diagnosis, treatment and coordination of patient care in this new rare disease market. In fact, over the last five years, we have seen a compound annual growth rate of 25 percent in the number of diagnosed SM patients observable in U.S. claims data, with more than 25,000 diagnosed patients in the U.S. today. Combined with recently published epidemiology data showing SM prevalence may be double than prior estimates, we believe there is a $4 billion peak opportunity for our SM franchise.   

And we have made important progress in advancing our franchise lifecycle strategy. In 2024, we initiated the registration-directed Phase 3 HARBOR trial of elenestinib, our next-generation KIT D816V inhibitor. Through strategic design of the HARBOR trial, we expect to drive further innovation in the treatment of ISM, with novel endpoints assessing bone health, anaphylaxis and markers of inflammation designed with input from the U.S. Food and Drug Administration (FDA). With our approach, we expect to clinically differentiate elenestinib, raising the bar from symptom control to disease modification, and deliver significant value to the growing SM market for many years into the future.  

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  1. Internal Blueprint Medicines analyses of U.S. claims data (as of 2024). 2. Bergstrom et al; Acta Oncologica (2024).   

BLU-808, our next potential driver of significant growth  

In 2024, we also advanced our broader mast cell therapy portfolio, with the rapid completion of a Phase 1 healthy volunteer study of BLU-808, our oral, highly potent and selective wild-type KIT inhibitor. We designed BLU-808 to enable a differentiated clinical profile, with tunable dosing that can dial-in clinical activity and manage on-target adverse events to optimize a favorable benefit-risk profile that supports chronic treatment.   

Supporting this approach, BLU-808 healthy volunteer data presented early this year showed BLU-808 was well-tolerated, had dose-dependent pharmacokinetics with multiple doses providing clear target coverage, and rapid, robust and sustained reductions in serum tryptase, a pharmacodynamic marker of mast cell activity. Based on this data, we are now initiating multiple clinical proof-of-concept trials to further characterize the broad potential of BLU-808 across multiple allergic and inflammatory diseases.  

Continued disciplined financial stewardship  

In 2024, we continued to prioritize investment in our most compelling programs with discipline. As we drove significant AYVAKIT revenue growth and advanced our pipeline of promising mast cell therapies, we also reduced our operating cash burn by more than 50 percent, and we expect further reductions in 2025. We ended the year with approximately $863.9 million in cash, with an additional $78.7 million received in the first

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quarter of 2025 from proceeds of our equity stake in IDRx, which was acquired by GSK. Together, we expect our disciplined approach to capital allocation and durable cash position to enable us to continue to sustainably invest in strategic growth opportunities.  

Achievement fueled by a talented team and an award-winning culture  

Blueprint Medicines was again recognized as an employer-of-choice in 2024. We were named to USA Today’s “Top Places to Work” list; to The Boston Globe’s “Top Places to Work in Massachusetts” list; as a Fortune “Future 50” honoree; and as a top employer in Switzerland by Top Employers Institute. Our achievements are a testament to the hard work and dedication of our almost 650 team members and I thank each of them for their unwavering commitment to the patients and communities we serve.   

Today our future is brighter than ever before. We have the right people, portfolio, capabilities and vision to bring forward medicines that solve important medical challenges, dramatically improve patient lives and create significant value for our stockholders in 2025 and beyond.  

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On behalf of our board of directors, team members, patients and healthcare partners, thank you for your continued support and investment in Blueprint Medicines. 

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Sincerely,

Kate Haviland
President, Chief Executive Officer, and Director
On Behalf of the Board of Directors

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Cambridge, Massachusetts
April 24, 2025

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Dear Stockholders,

You are cordially invited to attend the 2025 annual meeting of stockholders of Blueprint Medicines Corporation to be held on Wednesday, June 18, 2025, at 3:00 p.m., Eastern Daylight Time, virtually via live webcast at http://www.virtualshareholdermeeting.com/BPMC2025, where you will be able to vote electronically and submit questions. You will need the 16-digit control number included with these proxy materials to attend the annual meeting. At the annual meeting, stockholders will consider and vote on the following matters:

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In addition to the foregoing items of business, stockholders will be asked to consider and vote on any other business that may properly come before the annual meeting or any adjournment or postponement thereof.

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The foregoing items of business are more fully described in the proxy statement accompanying this notice.

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Stockholders of record at the close of business on April 21, 2025 will be entitled to notice of and to vote at the annual meeting or any adjournment or postponement thereof. We encourage you to access the annual meeting before it begins. Online check-in to access the meeting will start shortly before the meeting on June 18, 2025. By attending the annual meeting virtually at http://www.virtualshareholdermeeting.com/BPMC2025 you may vote electronically during the meeting even if you have previously returned a proxy. Stockholders will also have the opportunity to submit questions during the annual meeting through http://www.virtualshareholdermeeting.com/BPMC2025. A technical support telephone number will be posted on the log-in page that you can call if you encounter any difficulties accessing the virtual meeting during the check-in or during the meeting.

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We have elected to provide access to our proxy materials over the Internet under the Securities and Exchange Commission’s “notice and access” rules. We believe that providing our proxy materials over the Internet expedites stockholders’ receipt of proxy materials, lowers costs and reduces the environmental impact of our annual meeting.

We encourage all stockholders to attend the annual meeting online. However, whether or not you plan to attend the annual meeting, we encourage you to read this proxy statement and submit your proxy or voting instructions as soon as possible. Please review the instructions on each of your voting options described in the proxy statement.

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Thank you for your ongoing support and continued interest in Blueprint Medicines Corporation.

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By Order of the Board of Directors,

Tracey L. McCain, Esq.
Chief Legal and Compliance Officer

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Cambridge, Massachusetts
April 24, 2025

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Important Notice Regarding Internet Availability of Proxy Materials

We are furnishing proxy materials to our stockholders primarily via the Internet. On April 24, 2025, we mailed to our stockholders a Notice of Internet Availability, or Notice, containing instructions on how to access our proxy materials, including this proxy statement and our 2024 annual report to stockholders. The Notice also instructs you on how to submit your proxy or voting instructions through the Internet or to request a paper copy of our proxy materials, including a proxy card or voting instruction form that includes instructions on how to submit your proxy or voting instructions by mail or telephone. Other stockholders, in accordance with their prior requests, have received e-mail access to our proxy materials and instructions to submit their vote via the Internet, or have been mailed paper copies of our proxy materials and a proxy card or voting instruction form.

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A copy of this proxy statement and our 2024 annual report to stockholders are available at www.proxyvote.com.

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Internet distribution of our proxy materials is designed to expedite receipt by stockholders, lower the cost of the annual meeting, and conserve natural resources. However, if you would prefer to receive printed proxy materials, please follow the instructions included in the Notice. If you have previously elected to receive our proxy materials electronically, you will continue to receive these materials via e-mail unless you elect otherwise.

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CORPORATE GOVERNANCE

WE ARE PURPOSEFULLY EVOLVING OUR CORPORATE GOVERNANCE AS WE CONTINUE TO GROW

Our board of directors is committed to good corporate governance and routine stockholder engagement to inform the evolution of our governance as we continue to grow. We solicit feedback on governance matters twice annually from our top 30 stockholders, representing about 75 percent of outstanding shares, to inform discussions with our nominating and corporate governance committee and full board of directors throughout the year. Following is a summary of actions we have taken in recent years in response to shareholder feedback.   

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* Data is as of March 31, 2025. Dr. Lydon has notified us that he will not stand for reelection at the 2025 annual meeting of stockholders. See “Proposal 1 – Election of Directors” below.

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In addition, in 2024, our nominating and corporate governance committee and board of directors reviewed and discussed stockholder feedback regarding our classified board structure, as well as benchmark analyses of other publicly traded life science companies. The board determined that our current structure remains appropriate based on the company’s emerging high-growth profile and consistent with approximately 75% of NYSE and Nasdaq-listed biotechnology peers (approximately 430 companies). Our board of directors plans to periodically reassess the board structure in the future as the company continues to mature and welcomes the opportunity for additional stockholder engagement on this and other governance matters. 

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SUSTAINABILITY AND RISK MANAGEMENT

At Blueprint Medicines, we believe that when we work together, the impact of our collective efforts can make a profound difference for patients, our employees and the communities in which we live and work. We’re grounded in integrity, we lead with our core values and we’re inspired to make the world a better place. 

WE CONTINUE TO DRIVE OUR SUSTAINABILITY INITIATIVES FORWARD

We are committed to a sustainability strategy that prioritizes efforts in areas most closely aligned with our business. In 2024, we conducted a materiality assessment to evaluate perspectives from internal and external stakeholders around key environmental, social and governance (ESG) topics, which we plan to refresh approximately every five years. Aligned with the results of this assessment, we focus our disclosures around the following three key pillars.

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Commitment to patients: Delivering medicines to patients is our core business purpose, and we do this in a way that builds trust with the patient and healthcare provider communities. We are committed to ensuring patients can access our therapies, and we provide support programs that help patients in the U.S. to rapidly fill and afford their prescriptions, with dedicated case management support, co-pay assistance and free medicines for eligible patients. Additional programs have included global early access to investigational medicines for eligible patients and practices to enable diverse and representative clinical trial participation. Further, we are committed to protecting patient privacy by safeguarding clinical and commercial data across the company, consistent with best practices. 

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Attracting, engaging and retaining our employees: Knowing our employees are central to the strength of our business, we recruit and hire highly qualified talent with diverse skill sets, career and life experiences, and education, and we work hard to ensure our employees have the support they need to individually excel and achieve operational excellence together. We are intentional in how we build and nurture our culture, and cultivate a workplace that values well-being, continuous learning, and talent development tailored to individual employee interests in alignment with business needs. In doing so, we practice equity by treating all employees with fairness and working to ensure equal opportunity for current and potential employees. Importantly, we also celebrate the unique differences and varied life experiences of our employees so that we can sustain our diverse culture, which in turn fosters inclusion and belonging so that everyone feels welcome and accepted. Notable employee programs include comprehensive total rewards compensation and benefits, a robust learning and development curriculum, and mentoring and leadership training.

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Responsible business practices: We protect the company by planning ahead where possible and preparing for the unknown. In 2023, we updated cybersecurity initiatives and training to guard against cyber-attacks and safeguard our employee, patient and customer data. In 2024, we held over 30 company-wide and department- level artificial intelligence (AI) training sessions to raise awareness of the risks and responsible use of AI. All employees receive annual information security and privacy training, with 96% completion in 2024.

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REPORTING OF SUSTAINABILITY METRICS

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Since 2021, we have published an annual Sustainability Report to highlight our environmental, social and governance, or ESG, risk management initiatives. In May 2025, we will publish our fourth annual Sustainability Report for the 2024 calendar year. 

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Table Of Contents

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This proxy statement and the enclosed proxy card are being furnished in connection with the solicitation of proxies by the board of directors of Blueprint Medicines Corporation for use at the annual meeting of stockholders to be held online on Wednesday, June 18, 2025, at 3:00 p.m., Eastern Daylight Time, and at any adjournment or postponement thereof. The annual meeting will be held entirely online this year at http://www.virtualshareholdermeeting.com/BPMC2025. We encourage all stockholders to attend the annual meeting online. However, whether or not you plan to attend the annual meeting, we encourage you to read this proxy statement and submit your proxy or voting instructions as soon as possible. Additional details regarding attending the virtual annual meeting and voting at the meeting are provided below in section entitled “Frequently Asked Questions Regarding the Annual Meeting and Voting.”

Unless otherwise stated, all references to “us,” “our,” “Blueprint,” “Blueprint Medicines,” “we,” the “company” and similar designations refer to Blueprint Medicines Corporation and its consolidated subsidiaries. References to our website are inactive textual references only, and the contents of our website are not incorporated by reference into this proxy statement.

This proxy statement summarizes information about the proposals to be considered at the meeting and other information you may find useful in determining how to vote. The proxy card is the means by which you actually authorize another person to vote your shares in accordance with your instructions. We are making this proxy statement, the related proxy card and our 2024 annual report to stockholders available to stockholders for the first time on or about April 24, 2025.

A copy of our Annual Report on Form 10-K for the fiscal year ended December 31, 2024, as filed with the SEC, except for exhibits, will be furnished without charge to any stockholder upon written or oral request to Blueprint Medicines Corporation, 45 Sidney Street, Cambridge, Massachusetts 02139 or by calling 1-800-579-1639, by emailing sendmaterial@proxyvote.com or by submitting a request over the Internet at www.proxyvote.com. This proxy statement and our Annual Report on Form 10-K for the fiscal year ended December 31, 2024 are also available on the SEC’s website at www.sec.gov and the “Investors & Media—SEC Filings” section of our website, which is located at http://ir.blueprintmedicines.com.

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Our board of directors is divided into three classes, with one class of our directors standing for election each year. Directors in each class are elected at the annual meeting of stockholders held in the year in which the term for their class expires and hold office for a three-year term and until their resignation or removal or their successors are duly elected and qualified. In accordance with our certificate of incorporation and bylaws, our directors may fill existing vacancies on the board of directors.

The term of office of our Class I directors, Jeffrey W. Albers, Mark Goldberg, M.D., Nicholas Lydon, Ph.D., FRS, and John Tsai, M.D., will expire at the 2025 annual meeting of stockholders. The nominees for Class I directors for election at the 2025 annual meeting of stockholders are Mr. Albers, Dr. Goldberg, and Dr. Tsai. On April 21, 2025, Dr. Lydon notified us that he will not stand for reelection as a director at the 2025 annual meeting of stockholders. His service on our board of directors will therefore end at the 2025 annual meeting of stockholders. Dr. Lydon’s decision did not result from any disagreement with us on any matter relating to our operations, policies or practices. If any of Mr. Albers, Dr. Goldberg, and Dr. Tsai is elected at the 2025 annual meeting of stockholders, such individual will be elected to serve for a three-year term that will expire at our 2028 annual meeting of stockholders and until such individual’s successor is elected and qualified.

If no contrary indication is made, proxies in the accompanying form will be voted for Mr. Albers, Dr. Goldberg, and Dr. Tsai or, in the event that any of Mr. Albers, Dr. Goldberg and Dr. Tsai is not a candidate or is unable to serve as a director at the time of the election (which is not currently expected), for any nominee who is designated by our board of directors to fill the vacancy.

VOTE REQUIRED AND Recommendation of the Board of Directors

The three nominees receiving the highest number of affirmative votes of the shares present in person or represented by proxy at the 2025 annual meeting of stockholders and entitled to vote on the election of directors will be elected to the board of directors. If a nominee receives a greater number of votes “withheld” than votes “for” such election, the nominee is required to promptly tender their resignation to the board of directors in accordance with our director resignation policy, as described in our corporate governance guidelines. The nominating and corporate governance committee will consider all factors it deems relevant in determining whether to recommend to the board of directors to accept any resignation offer. The board of directors will act on the nominating and corporate governance committee’s recommendation within 90 days following certification of the election results. In deciding whether to accept the resignation offer, the board of directors will evaluate the factors considered by the nominating and governance committee and any additional information and factors that the board of directors believes to be relevant. The company will promptly publicly disclose the board of directors’ decision in a periodic or current report filed with the SEC.

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Votes withheld from any director are counted for purposes of determining the presence or absence of a quorum, but have no other legal effect under Delaware law. Broker non-votes will have no effect on the outcome of this proposal.

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Information Regarding Directors

Set forth below are the names and certain information for each member of our board of directors, including the nominees for election as Class I directors, as of March 31, 2025. The information presented includes each director’s and nominee’s principal occupation and business experience for the past five years, and the names of other public companies of which the individual has served as a director during the past five years. The information presented below regarding the specific experience, qualifications, attributes and skills of each director and nominee led our board of directors to conclude that the individual should serve as a director. In addition, we believe that all of our directors and nominees possess the attributes or characteristics that the nominating and corporate governance committee expects of each director, which are described under the section titled “—Director Nomination Process.”

There are no family relationships among any of our directors or executive officers.

(1) Member of the audit committee. (2) Member of the compensation committee. (3) Member of the nominating and corporate governance committee.

*Dr. Lydon has notified us that he will not stand for reelection as a director at the 2025 annual meeting of stockholders. See “Proposal 1 – Election of Directors” above.

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CLASS I DIRECTOR NOMINIEES
TERM EXPIRING AT THE 2025 ANNUAL MEETING OF STOCKHOLDERS

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CLASS II DIRECTORS

TERM EXPIRING AT THE 2026 ANNUAL MEETING OF STOCKHOLDERS

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CLASS III DIRECTORS
TERM EXPIRING AT THE 2027 ANNUAL MEETING OF STOCKHOLDERS

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Corporate Governance

Our board of directors believes that good corporate governance is important to ensure that our company is managed for the long-term benefit of stockholders. This section describes key corporate governance guidelines and practices that our board of directors has adopted.

CORPORATE GOVERNANCE HIGHLIGHTS

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CORPORATE GOVERNANCE STRENGTHS

We are committed to exercising good corporate governance practices. We believe that good governance promotes the long-term interests of our stockholders and strengthens the accountability of our board of directors and management. Our corporate governance practices are primarily designed to:

* This figure is based on the Nasdaq Listing Rules for director independence.

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CORPORATE GOVERNANCE MATERIALS

Complete copies of our corporate governance guidelines, committee charters and code of conduct are available on the “Investors & Media — Corporate Governance” section of our website, which is located at http://ir.blueprintmedicines.com. Alternatively, you can request a copy of any of these documents by contacting us at Blueprint Medicines Corporation, 45 Sidney Street, Cambridge, Massachusetts 02139, Attn: Investor Relations, telephone: (617) 374-7580, e-mail: ir@blueprintmedicines.com.

CODE OF BUSINESS CONDUCT AND ETHICS AND CORPORATE GOVERNANCE GUIDELINES

Our board of directors has adopted a written code of business conduct and ethics that applies to our directors, officers and employees, including our principal executive officer, principal financial officer, principal accounting officer or controller, and persons performing similar functions. A copy of our code of business conduct and ethics is

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available on the “Investors & Media — Corporate Governance” section of our website, which is located at http://ir.blueprintmedicines.com. We intend to disclose on our website any amendments to, or waivers from, our code of business conduct and ethics that are required to be disclosed pursuant to the disclosure requirements of Item 5.05 of Form 8-K.

Our board of directors has also adopted corporate governance guidelines to assist in the exercise of its duties and responsibilities and to serve the best interests of our company and our stockholders, which we periodically review and update, with the most recent update occurring in 2024. A copy of our corporate governance guidelines is available on the “Investors & Media — Corporate Governance” section of our website, which is located at http://ir.blueprintmedicines.com.

DIRECTOR RESIGNATION POLICY

In 2024, in response to stockholder feedback, we implemented a director resignation policy, which is set forth in our corporate governance guidelines, a copy of which is available on the “Investors & Media — Corporate Governance” section of our website. The policy establishes that any director nominee who receives a greater number of “withhold” votes than “for” votes in an uncontested election of directors is required to tender their resignation promptly following the certification of the election results. Abstentions and broker non-votes, if any, are not counted as either a “withhold” or “for” vote.

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The nominating and corporate governance committee will promptly consider whether to accept or reject the resignation offer, or whether other action should be taken, and make a recommendation to the board of directors. The board of directors will act on the recommendation of the nominating and corporate governance committee no later than 90 days following the certification of the election results. In deciding whether to accept the resignation offer, the board of directors will evaluate the factors considered by the nominating and corporate governance committee and any additional information and factors that the board of directors believes to be relevant. Any director who tenders a resignation offer pursuant to the director resignation policy will not participate in the proceedings of either the nominating and corporate governance committee or the board of directors with respect to their own resignation offer. However, the director will remain active and engaged in all other activities of the board of directors, deliberations and decisions of the board of directors and its committees during the evaluation process conducted by the nominating and corporate governance committee and board of directors.

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We will promptly publicly disclose the board of directors’ decision and, if applicable, the reasons for rejecting the tendered resignation in a periodic or current report filed with the SEC.

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RISK OVERSIGHT

Our board of directors oversees the management of risks inherent in the operation of our business and the implementation of our business strategies. Our board of directors performs this oversight role by using several different levels of review. In connection with reviews of the operations and corporate functions of our company, our board of directors addresses the primary risks associated with those operations and corporate functions. In addition, our board of directors reviews the risks associated with our company’s business strategies periodically throughout the year as part of its consideration of undertaking any such business strategies.

Each committee of our board of directors also oversees the management of our company risk that falls under the committee’s particular purview and within its areas of responsibility. In performing this function, each committee has full access to management, as well as the ability to engage advisors. Our audit committee oversees our policies and programs related to our financial and accounting systems, accounting policies and investment strategies, internal audit function, investment strategies and cybersecurity. With respect to cybersecurity risk, our audit committee receives periodic updates from the company’s information security team, which include bi-annual presentations on the status of our cybersecurity risk management program by the senior vice president, information systems. These reports include updates on our performance preparing for, preventing, detecting, responding to and recovering from cyber incidents, if any. The audit committee also is responsible for addressing risks arising from related party transactions, if any. In connection with its risk management role, our audit committee meets privately with representatives from our independent registered public accounting firm and certain members of our executive team, as and when needed. The audit committee oversees the operation of our risk management program,

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including the identification of the primary risks associated with our business and periodic updates to such risks, and reports to our board of directors regarding these activities. Our compensation committee oversees risks associated with our compensation policies and practices to help ensure that such policies and practices do not incentivize or encourage excessive risk-taking, and periodically assists our board of directors in its oversight of human capital management policies and strategies, including those regarding recruiting, retention, and career development. Our nominating and corporate governance committee oversees risks related to our governance structure and succession planning, and our environmental, social and governance risk and reporting.

BOARD DETERMINATION OF INDEPENDENCE

Our board of directors annually undertakes a review of the composition of our board of directors and its committees and the independence of each director. Based upon information requested from and provided by each director concerning their background, employment and affiliations, including family relationships, our board of directors has determined that each of our directors, with the exception of Jeffrey W. Albers and Kathryn Haviland, is an “independent director” as defined under Rule 5605(a)(2) of the Nasdaq Listing Rules. Mr. Albers is not an independent director under Rule 5605(a)(2) because he was employed as our president and chief executive officer through April 3, 2022 and as our executive chairman through December 31, 2022, and was engaged as a consultant to the company until December 31, 2023. Ms. Haviland is not an independent director under Rule 505(a)(2) because she is currently employed as our president and chief executive officer and was previously employed as our chief operating officer from January 2019 through April 2022, and as our chief business officer from January 2016 to January 2019. Our board of directors also determined that each of: Daniella Beckman, Lonnel Coats and Mark Goldberg, who comprise our audit committee; Lynn Seely, Habib Dable and Mark Goldberg, who comprise our compensation committee; and Lonnel Coats, Habib Dable and Lynn Seely, who comprise our nominating and corporate governance committee, satisfies the independence standards for such committees established by the SEC and the Nasdaq Listing Rules, as applicable, including in the case of all members of the audit committee, the independence requirements contemplated by Rule 10A-3 under the Securities Exchange Act of 1934, or the Exchange Act, and in the case of all members of the compensation committee, the independence requirements contemplated by Rule 10C-1 under the Exchange Act. In making such determinations, our board of directors considered the relationships that each such non-employee director has with our company and all other facts and circumstances our board of directors deemed relevant in determining independence, including the beneficial ownership of our capital stock by each non-employee director.

DIRECTOR NOMINATION PROCESS

The process followed by our nominating and corporate governance committee of our board of directors to identify and evaluate qualified director candidates includes requests to board members and others for recommendations, meetings from time to time to evaluate biographical information and background material relating to potential candidates and interviews of selected candidates by members of the nominating and corporate governance committee and our board of directors.

DIRECTOR CRITERIA, QUALIFICATIONS, AND EXPERIENCE

In considering whether to recommend to our board of directors any candidate for inclusion in our board of directors’ slate of recommended director nominees, including candidates recommended by stockholders, the nominating and corporate governance committee applies the criteria set forth in our corporate governance guidelines. These criteria include, without limitation, the candidate’s experience at a strategic or policymaking level in a business, government, non-profit or academic organization of high standing, accomplishments in the candidate’s respective field, the candidate’s reputation for high ethical and moral standards, the candidate’s time and ability to devote to the affairs of the company, and to the extent applicable, the candidate’s history of actively contributing to any boards of directors on which the candidate previously served.

Our nominating and corporate governance committee and our board of directors know that a diversity of skills, experiences, perspectives and backgrounds across our organization, including our board of directors, helps us to

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solve complex scientific, medical and business challenges inherent to the biopharmaceutical sector. Accordingly, as noted in our corporate governance guidelines, the board is committed to a diversified membership, and in addition to the criteria referenced above, the nominating and corporate governance committee will also consider all facts and circumstances that it deems appropriate or advisable, including, among other things, the skills of the prospective director candidate, his or her depth and breadth of business experience and other background characteristics. Our nominating and corporate governance committee’s and our board of directors’ priority in selecting board members is identification of highly-qualified individuals who will further the interests of our stockholders. Core to operating our business is our commitment to integrating diverse skill sets, career and life experiences, and education to solve complex scientific, medical and business challenges inherent in driving innovation, and we actively seek directors representing this diversity. Our holistic approach not only enriches our organization’s composition but also fuels our innovation and drives our success.

The director biographies on pages 4-13 of this proxy statement provide details regarding each nominee’s experience, qualifications, attributes and skills that led our nominating and corporate governance committee and our board of directors to conclude such individual should continue to serve as a director. Our nominating and corporate governance committee and our board of directors believe that each of the nominees has the individual attributes and characteristics required of each of our directors, and the nominees collectively possess the breadth of skill sets and specific experience desired of our board of directors as a whole.

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The following table and pie charts provide information regarding the depth, breadth and diversity of experience and background of our board of directors:

* Dr. Lydon has notified us that he will not stand for reelection as a director at the 2025 annual meeting of stockholders. See “Proposal 1 – Election of Directors” above.

**    Ms. Beckman and Mr. Coats are our designated audit committee financial experts, pursuant to SEC rules and regulations.

***  The Blueprint board leadership designation includes chairperson of the board, lead independent director and/or chair of a board committee.

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* As of March 31, 2025.

STOCKHOLDER NOMINATIONS

Stockholders may recommend individuals to our nominating and corporate governance committee for consideration as potential director candidates by submitting their names, together with appropriate biographical information and background materials and a statement as to the amount of our beneficially owned common stock held by the stockholder or group of stockholders making the recommendation as of the date such recommendation is made, to Blueprint Medicines Corporation, Attention: Nominating and Corporate Governance Committee, 45 Sidney Street, Cambridge, Massachusetts 02139. Assuming that appropriate biographical and background material has been provided on a timely basis, the nominating and corporate governance committee will evaluate stockholder-recommended candidates by following substantially the same process, and applying substantially the same criteria, as it follows for candidates submitted by others. If the board of directors determines to nominate a stockholder-recommended candidate and recommends their election, then their name will be included in our proxy card for the next annual meeting.

Our amended and restated bylaws, or bylaws, also provide for proxy access that allows qualifying stockholders to directly nominate director candidates for consideration at an annual meeting of stockholders and have such candidate be included in our proxy materials for the applicable annual meeting. The key elements of our proxy access bylaw provisions are as follows:

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The above list is only a summary of our proxy access provisions in our bylaws and is qualified in its entirety by our bylaws. A stockholder who wishes to nominate a proxy access nominee to be considered for election as a director at the 2025 annual meeting of stockholders must follow the procedures set forth in our bylaws as well as under “Stockholder Proposals.”

BOARD LEADERSHIP STRUCTURE

Under our corporate governance guidelines, the positions of chairperson of our board of directors and of chief executive officer may, but need not be, the same person. Additionally, our corporate governance guidelines provide that if the chairperson of the board of directors is not an independent director, then the independent directors may elect one independent director to serve as the lead independent director.

Jeffrey W. Albers has served as a director since 2014 and as the chairperson of our board of directors since June 2021. Mr. Albers possesses detailed and first-hand knowledge of the issues, opportunities, and challenges facing our business, making him well-suited to preside over meetings of, and oversee, our board of directors. Because Mr. Albers was employed by us in his role as president and chief executive officer through April 3, 2022, continued to be employed by us in his role as executive chairman through December 31, 2022, and was engaged as a consultant to the company until December 31, 2023, our board of directors does not currently consider him to be “independent” in his role as chairperson of the board of directors. Accordingly, in June 2021, our board of directors designated Lynn Seely as our lead independent director. Dr. Seely’s service as lead independent director provides an effective independent voice in our leadership structure, encouraging objective oversight of management’s performance and enhancing the effectiveness of the board of directors as a whole. As lead independent director, Dr. Seely presides over meetings of our independent directors, serves as a liaison between our chairperson and the independent directors and performs such additional duties as our board of directors may otherwise determine and delegate.

Our board of directors has three standing committees that currently consist of, and are chaired by, independent directors. Our board of directors delegates substantial responsibilities to the committees, which then report their activities and actions back to the full board of directors. We believe that the independent committees of our board of directors and their chairpersons promote effective independent governance. Meanwhile, the extensive company-specific experience and expertise of Mr. Albers and Ms. Haviland, together with the outside experience, oversight and expertise of our independent directors, allows for differing perspectives and roles regarding strategy development that benefit our stockholders.

We believe that our current leadership structure provides effective independent director oversight of management, while allowing our board to benefit from Mr. Albers’ and Ms. Haviland’s experience and leadership in our business, enabling Mr. Albers and Ms. Haviland to act as key links between our board of directors and other members of management and enhancing our ability to communicate our strategy clearly and consistently to our investors, employees and partners. We and our board of directors continue to review the leadership structure of the board on a regular basis.

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BOARD OF DIRECTOR MEETINGS AND ATTENDANCE

Our board of directors held ten (10) meetings and acted by unanimous written consent twice during the year ended December 31, 2024. During the year ended December 31, 2024, each director attended at least 75% of the aggregate of (i) all meetings of the board and (ii) all meetings of the committees of the board of directors on which such director then served.

Although we do not have a formal policy regarding attendance by members of our board of directors at our annual meeting of stockholders, we encourage all of our directors to attend. All members of our board of directors who were then directors attended our 2024 annual meeting of stockholders.

COMMITTEES OF THE BOARD OF DIRECTORS

We have established an audit committee, a compensation committee, and a nominating and corporate governance committee. Each of these committees operates under a charter that has been approved by our board of directors. A copy of each committee’s charter can be found under the “Investors & Media — Corporate Governance” section of our website, which is located at http://ir.blueprintmedicines.com.

AUDIT COMMITTEE

Our audit committee’s responsibilities include:

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The current members of our audit committee are Daniella Beckman, Lonnel Coats and Mark Goldberg. Ms. Beckman serves as chair of the audit committee. Our board of directors has determined that each of Ms. Beckman and Mr. Coats qualifies as an audit committee financial expert within the meaning of applicable SEC rules. The audit committee held five (5) meetings during the year ended December 31, 2024, and each meeting was attended by all of the members of our audit committee.

COMPENSATION COMMITTEE

Our compensation committee’s responsibilities include:

The current members of our compensation committee are Lynn Seely, Habib Dable and Mark Goldberg. Dr. Seely serves as chair of the compensation committee. During the year ended December 31, 2024, the compensation committee held ten (10) meetings, one (1) joint meeting with the board of directors and acted by unanimous written consent six (6) times (including five (5) written consents approving monthly inducement grants to new hires as required by the inducement grant exception prior to the adoption of our 2024 Plan) during the year ended December 31, 2024. Each member of the compensation committee attended at least 75% of all the compensation committee meetings held during the year ended December 31, 2024.

The compensation committee may delegate its authority to an officer or a committee of one or more officers, including our chief executive officer, to grant certain equity awards to certain individuals, and our compensation committee has delegated such authority to Ms. Haviland with respect to certain equity awards. For more information, please see “Compensation Discussion and Analysis—Overview of Executive Compensation Process.”

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NOMINATING AND CORPORATE GOVERNANCE COMMITTEE

Our nominating and corporate governance committee’s responsibilities include:

The current members of our nominating and corporate governance committee are Lonnel Coats, Habib Dable and Lynn Seely. Mr. Coats serves as chair of the nominating and corporate governance committee. The nominating and corporate governance committee held four (4) meetings and did not act by unanimous written consent during the year ended December 31, 2024. Each member of the nominating and corporate governance committee attended at least 75% of all the nominating and corporate governance committee meetings held during the year ended December 31, 2024.

COMMUNICATING WITH THE BOARD OF DIRECTORS

Our board of directors will give appropriate attention to written communications that are submitted by stockholders or other interested parties and will respond if and as appropriate. The chairperson of the board of directors is primarily responsible for monitoring communications from stockholders and other interested parties and for providing copies or summaries to the other directors as the chairperson considers appropriate.

Stockholders who wish to send communications on any topic to our board of directors (or any individual director) should address such communications to Blueprint Medicines Corporation, Attention: Board of Directors, 45 Sidney Street, Cambridge, Massachusetts 02139. Upon receipt of such communications, the correspondence will be directed to the appropriate person, including individual directors. A copy of any such written communication may also be forwarded to the company’s legal counsel and a copy of such communication may be retained for a reasonable period of time. You may submit your concern anonymously or confidentially.

The audit committee oversees the procedures for the receipt, retention, and treatment of complaints received by the company regarding accounting, internal accounting controls or auditing matters, and the confidential, anonymous submission in the United States, and elsewhere as permitted by law, by employees of concerns regarding questionable accounting or auditing matters. The company has also established a toll-free telephone number, the “BlueCares” hotline, for the reporting of such activity, which is (844) 857-5642 or you can visit Blueprintmedicines.ethicspoint.com to submit any questions or concerns.

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BOARD RESPONSE TO STOCKHOLDER FEEDBACK

Following our 2024 annual meeting, we reached out to our top 30 stockholders, representing approximately 75% of our shares outstanding, to proactively engage in discourse around corporate governance matters and other topics that may be important to our stockholders. Through this engagement, we received verbal or written feedback from stockholders representing approximately 60% of our shares outstanding.  Included in these meetings were our Chief Operating Officer; Senior Vice President, Corporate Affairs; Senior Vice President, Total Rewards and People Operations; Vice President, Investor Relations; Vice President, Corporate Legal Affairs; and as appropriate, certain members of our board of directors.

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Through these discussions, stockholders recognized our evolution over the last several years of corporate governance provisions in response to stockholder feedback and our implementation of routine, structured twice annual stockholder engagement on governance matters, and they encouraged us to continue these practices.  In addition, some stockholders expressed a desire for declassifying our board of directors. Subsequently, our nominating and corporate governance committee and full board of directors reviewed and discussed this feedback, as well as benchmark analyses of other publicly traded life science companies. The board determined that the current structure remains appropriate based on the company’s emerging high-growth profile and consistent with approximately 75% of NYSE and Nasdaq-listed biotechnology peers (approximately 430 companies), including a subset of emerging commercial-stage biotechnology peers. Our board of directors plans to periodically reassess the classified board structure in the future as the company continues to mature and welcomes opportunity for additional stockholder engagement on this and other governance matters.

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Director Compensation

Our board of directors has adopted a non-employee director compensation policy, which is designed to provide a total compensation package that enables us to attract and retain, on a long-term basis, high caliber non-employee directors. In June 2024, our board of directors amended and restated our non-employee director compensation policy as a result of competitive benchmarking and peer company compensation levels and design practices. The table below provides information for the policy pursuant to which compensation was paid to our non-employee directors before and after June 2024.

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The stock options granted to our non-employee directors will have an exercise price equal to the closing price of our common stock as reported on the Nasdaq Global Select Market on the date of grant and will expire ten years after the date of grant. Any non-employee director who has not served as a member of the board of directors for the 12 months prior to the date of grant for an annual equity award will have the award pro-rated to reflect the number of months (and partial months) of such individual’s service as a member of the board of directors during such 12 month period. The initial stock options granted to new non-employee directors will vest in equal monthly installments over a three-year period following the grant date. The initial restricted stock units, or RSUs, granted to new non-employee directors will vest in equal annual installments over a three-year period beginning on the one-year anniversary of the grant date. The annual stock options and the annual RSUs granted to our non-employee directors will vest in full upon the earlier of the first anniversary of the date of grant or the date of the following annual meeting of stockholders. Any initial and annual equity awards granted to each of our non-employee

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directors will automatically accelerate and become fully vested and exercisable upon the non-employee director’s termination due to death or disability or upon a sale event (as defined in the 2024 Plan and the 2015 Plan, as applicable). In addition, each non-employee director has the right to elect to receive all or a portion of their annual cash compensation under the non-employee director compensation policy in the form of RSUs. Any such election must be made before the start of our fiscal year and any such RSU will vest quarterly over a one-year period. Except as mentioned above, vesting of all stock options and RSUs is subject to the non-employee director’s continued service on the board of directors or subject to continued service as a consultant, director or employee of the company or any of its affiliates, as applicable. In addition, our 2024 Plan provides that the value of awards to a non-employee director in any calendar year shall not exceed: (i) $1,000,000 in the first calendar year an individual becomes a non-employee director and (ii) $750,000 in any other calendar year. For the purpose of this limitation, the value of any award shall be its grant date fair value, as determined in accordance with ASC Topic 718 or successor provision but excluding the impact of estimated forfeitures related to service-based vesting provisions.

All cash fees will be paid quarterly, in arrears, or upon the earlier resignation or removal of the non-employee director. The amount of each payment will be prorated for any portion of a quarter that a non-employee director is not serving on our board of directors, based on the number of calendar days served by such non-employee director.

Each non-employee director is also entitled to reimbursement for reasonable travel and other expenses incurred in connection with attending meetings of the board of directors and any committee on which the director serves.

We have adopted stock ownership guidelines designed to ensure that our directors and senior executive officers are focused on both short- and long-term objectives and to better align their interests with other stockholders. Under our current stock ownership guidelines, shares underlying vested and unexercised “in-the-money” stock option awards are excluded from the calculation of requisite stock ownership levels for the covered parties. All of our directors are in compliance with our current stock ownership guidelines. See “Other Compensation Policies and Practices – Stock Ownership Guidelines” for more information.

The following table sets forth a summary of the compensation for our non-employee directors during 2024.

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We are providing our stockholders the opportunity to vote to approve, on an advisory non-binding basis, the compensation of our named executive officers as disclosed in this proxy statement in accordance with the SEC’s rules. This proposal, which is commonly referred to as “say-on-pay,” is required by the Dodd-Frank Act, which added Section 14A to the Exchange Act. Our executive compensation program is designed to reward value creation for stockholders and to attract, motivate, and retain a highly skilled team of executive officers, who are critical to our success. Under this program, our named executive officers are rewarded for the achievement of our short- and long-term strategic and financial goals, which we believe serves to enhance short- and long-term value creation for our stockholders.

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The section of this proxy statement titled “Executive Compensation” beginning on page 32, including “Compensation Discussion and Analysis,” describes in detail our executive compensation program and the decisions made by our compensation committee with regard to such program. As we describe in greater detail in the “Compensation Discussion and Analysis” section, we generally strive to provide our named executive officers with a mix of short-term and long-term performance-based incentives to encourage consistently strong performance, and our board of directors believes that this link between compensation and the achievement of our near- and long-term business goals has helped drive our performance over time. At the same time, we believe our program does not encourage excessive risk-taking by management. 

Our board of directors is asking stockholders to approve the following resolution:

RESOLVED, that the stockholders of Blueprint Medicines Corporation approve, on a non-binding advisory basis, compensation paid to the company’s named executive officers, as disclosed pursuant to Item 402 of Regulation S-K, including the “Compensation Discussion and Analysis,” the compensation tables and narrative discussion included therein.

You are being asked to approve on a non-binding advisory basis, the compensation paid to our named executive officers as set forth in the Compensation Discussion and Analysis, Summary Compensation Table and related notes and narrative set forth in this proxy statement. This vote is not intended to address any specific compensation item, but rather the overall compensation paid to our named executive officers and the philosophy, policies and practices described herein.

Vote Required and RECOMMENDATION OF THE BOARD OF DIRECTORS

Approval of this resolution requires the affirmative vote of a majority of the votes cast on this proposal. As a non-binding advisory vote, the outcome of the vote on this proposal is non-binding and does not overrule any decision by the company or the board of directors (or any committee thereof), create or imply any change to the fiduciary duties of the company or the board of directors (or any committee thereof), or create or imply any additional fiduciary duties for the company or the board of directors (or any committee thereof). However, our compensation committee and board of directors value the opinions expressed by our stockholders in their vote on this proposal and intend to consider carefully the outcome of the vote when making future compensation decisions for named executive officers. Abstentions and broker non-votes will have no effect on the outcome of this proposal.

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Executive Officers

Certain information regarding our executive officers who are not also directors, as of March 31, 2025, is set forth below.

Percy H. Carter, M.B.A., Ph.D. has served as our chief scientific officer since May 2021. Dr. Carter previously served as chief scientific officer at FibroGen, Inc. from September 2020 to May 2021. From June 2019 to September 2020, he served as global head of discovery sciences at Janssen Pharmaceuticals, Inc., a division of Johnson & Johnson, where he led more than 700 employees comprising several key research and discovery functions and drove the synthetic discovery strategy in collaboration with partners across various therapeutic areas. From August 2001 to May 2019, Dr. Carter held roles of increasing responsibility in drug discovery, covering all therapeutic areas, drug platforms and stages of discovery at Bristol-Myers Squibb Company, or BMS. This included serving as senior vice president and head of discovery between November 2018 and May 2019, and head of discovery chemistry & molecular technologies from October 2016 to November 2018. Prior to his experience at BMS, he was senior research scientist in chemical and physical sciences at DuPont Pharmaceuticals Company, until it was acquired by BMS in 2001. Dr. Carter is an inventor or co-inventor on 28 U.S. patents and has authored or co-authored more than 80 peer-reviewed publications. Dr. Carter has served as a member of the board of directors of Cellarity since 2024 and previously served as a member of the board of directors of HiFiBio Therapeutics from 2022 to 2025. Dr. Carter currently serves as the chairman of the board of the Wood Hudson Cancer Research Laboratory. Dr. Carter received an A.B. in Chemistry from Dartmouth College and a Ph.D. in Organic Chemistry from Harvard University. In addition, he received an M.B.A. from Massachusetts Institute of Technology.

Debra Durso-Bumpus has served as our chief people officer since February 2020. She has been with us since April 2015 as a member of the executive team and previously served as our senior vice president, human resources. Bringing nearly 20 years of experience focused on providing strategic direction to companies on people matters, managing rapid growth and creating and maintaining high performance cultures, Ms. Durso-Bumpus has operated in a number of leadership positions. Prior to joining Blueprint Medicines, she served as the interim head of human resources at Cubist Pharmaceuticals, Inc. or Cubist, where she was appointed to lead the post-merger human resources integration following the acquisition of Cubist by Merck & Co. Between April 2009 and the acquisition, Ms. Durso-Bumpus served as the global senior director for talent management and organizational development at Cubist, where she was primarily responsible for building talent and leadership strength and depth while managing change on a global scale to create a cohesive and highly differentiated culture. Prior to Cubist, she served as the North American manager of talent acquisition and workforce planning at Holcim, Inc., in Waltham, MA. Ms. Durso-Bumpus serves as a member of the board of directors for the Massachusetts Biotechnology Education Foundation, a nonprofit organization committed to supporting science and biotechnology education in Massachusetts through school programs, workforce training and lifelong learning. Ms. Durso-Bumpus received a B.S. in business management from Bentley University.

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Becker Hewes, M.D. has served as chief medical officer since January 2021. Dr. Hewes previously served as our senior vice president of clinical development from May 2020 to January 2021. Prior to joining us, he served as chief medical officer of Repertoire Immune Medicines, Inc. from February 2017 to May 2020, where he built their multidisciplinary clinical and biomarker team and advanced its immuno-oncology programs into clinical development. From June 2013 to February 2017, Dr. Hewes served as executive director of translational clinical oncology at the Novartis Institutes for BioMedical Research, or Novartis, where he led clinical development and translational medicine efforts for multiple early-stage oncology programs through clinical proof-of-concept, including Kisqali® (ribociclib), a targeted therapy approved to treat breast cancer, and other programs combining novel therapies. Prior to joining Novartis, he held roles of increasing responsibility related to clinical development in oncology and hematology within AstraZeneca PLC, Genzyme Corporation (which was later acquired by Sanofi S.A.) and Wyeth Pharmaceuticals Inc., including leading registration programs for Bosulif^® (bosutinib) and Torisel^® (temsirolimus) for chronic myelogenous leukemia and mantle cell lymphoma, respectively. Before joining industry, he conducted immuno-oncology research at the Emory Vaccine Center while treating patients as a pediatric oncologist at Children’s Healthcare of Atlanta. Dr. Hewes holds an M.D. from the Georgetown University of Medicine and a B.S. from Vanderbilt University.

Ariel Hurley has served as our senior vice president, finance and principal accounting officer since January 2023. Ms. Hurley previously served as our vice president, finance, and controller and principal accounting officer from March 2019 to December 2022, as our senior director, controller from January 2016 to February 2019 and as our director, controller from September 2014 to December 2015. Prior to joining us, from December 2005 to September 2014, Ms. Hurley served in various accounting and finance roles at Millennium Pharmaceuticals, Inc. (now a wholly-owned subsidiary of Takeda Pharmaceutical Company Limited). Ms. Hurley began her career at Deloitte & Touche, LLP and earned her certified public accountant license in Massachusetts. Ms. Hurley received a B.S. in accounting from Providence College.

Michael Landsittel, M.B.A. has served as our chief financial officer since January 2019. Mr. Landsittel previously served as our vice president, finance from February 2016 to January 2019 and as our senior director, finance from September 2014 to February 2016. Prior to joining us, Mr. Landsittel served as senior director of finance at Algeta ASA, from October 2012 to July 2014, where he led the U.S. organization’s finance and operations efforts, which ultimately supported the successful launch of the prostate cancer drug XOFIGO® (radium Ra 223 dichloride). Before joining Algeta ASA, from March 2012 to October 2012, he was the director of financial planning at Infinity Pharmaceuticals, Inc., or Infinity, where he was responsible for budgeting and forecasting, including support of Infinity’s long-range planning and capital markets activities. Prior to Infinity, from August 2002 to March 2012, Mr. Landsittel held multiple business development and strategic planning roles of increasing responsibility at Genzyme Corporation (which was later acquired Sanofi S.A.). Mr. Landsittel began his career at Arthur Andersen LLP, and is a registered certified public accountant in Illinois. Mr. Landsittel received a B.B.A from the University of Michigan and an M.B.A. from the Tuck School of Business at Dartmouth College.

Philina Lee, Ph.D. has served as our chief commercial officer since April 2022. Dr. Lee previously served as our senior vice president, head of portfolio strategy and program management from January 2021 to April 2022, where she was responsible for providing strategic and operational leadership across the company’s portfolio, our vice president, marketing and precision medicine from August 2019 to December 2020, our vice president, commercial strategy and operations from July 2017 to August 2019 and as our senior director, new product strategy and development from August 2014 to June 2017. During her tenure, Dr. Lee has been instrumental in building the company’s portfolio from research-stage onwards, laying the groundwork for the commercial strategy that is driving the successful launches of AYVAKIT® (avapritinib) and GAVRETO® (pralsetinib). Previously, Dr. Lee held product strategy and marketing roles of increasing responsibility at Algeta ASA, Sanofi S.A. and Genzyme Corporation (which was later acquired by Sanofi S.A.). Dr. Lee served on the board of Fusion Pharmaceuticals from February 2021 to June 2024. Dr. Lee earned a B.S. in biochemistry from the University of Alberta, and a Ph.D. in cell biology from the Massachusetts Institute of Technology.

Tracey L. McCain, Esq. has served as our executive vice president and chief legal officer since September 2016 and as our chief compliance officer since June 2017. Prior to joining us, from January 2016 to September 2016, Ms. McCain served as senior vice president and head of legal of Sanofi Genzyme, a global business unit of Sanofi S.A., or Sanofi, Ms. McCain held roles of increasing responsibility after joining Genzyme Corporation in May 1997, including becoming its general counsel after Genzyme Corporation was acquired by Sanofi in 2011. In her capacity

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as senior vice president and general counsel of Genzyme Corporation from May 2011 to December 2015, she oversaw all aspects of its legal department in the United States and Europe, including general corporate, commercial and intellectual property matters, and support of business development initiatives. Prior to Genzyme’s acquisition, Ms. McCain was also responsible for managing the securities and employment law teams and support of non-patent litigation. Before joining Genzyme, Ms. McCain was an associate at the law firm Palmer & Dodge LLP. Ms. McCain has served as a member of the board of directors of Kiniksa Pharmaceuticals, Ltd. since February 2018 and currently serves on its audit committee. She also served as a member of the board of directors of ImmunoGen, Inc. and sat on its audit committee from November 2021 to February 2024 when ImmunoGen, Inc. was acquired by AbbVie, Inc. She also serves on the board of trustees of the Dana Farber Cancer Institute. Ms. McCain holds a B.A. from the University of Pennsylvania with a major in political science and a J.D. from Columbia University School of Law.

Fouad Namouni, M.D. has served as our president, research and development, since September 2020. Prior to joining us, Dr. Namouni served in leadership roles at Bristol Myers Squibb Company since 1999, including as the global development lead for the its practice-changing cancer immunotherapy franchise. Most recently, he served as senior vice president and head of oncology development from August 2016 to April 2020 with the responsibility for driving product development plans from early-stage clinical development through commercialization across a portfolio of nearly 30 drug candidates. Previously, Dr. Namouni served as head of global medical affairs overseeing 1,700 employees worldwide from September 2015 to September 2017 and head of development for OPDIVO® (nivolumab) and YERVOY® (ipilimumab), immunotherapy medications used in the treatment of cancer, from January 2011 to September 2015. Dr. Namouni brings more than 20 years of oncology and cancer immunotherapy drug development expertise, as well as clinical experience as a pediatric oncologist. Dr. Namouni has served on the board of directors of Vor Biopharma Inc. since May 2024, and is a member of the nominating and corporate governance committee. He holds an M.D. from the University of Annaba Medical School in Algeria and a Pediatrics degree from Université Rene Descartes in Paris, France. Additionally, Dr. Namouni received a Pediatric Oncology and Hematology degree and an M.S. in clinical and experimental pharmacology from Université Paris-Sud in France.

Christina Rossi, M.B.A. has served as our chief operating officer since April 2022. She previously served as our chief commercial officer from October 2018 to April 2022 and has overseen the commercial launches of AYVAKIT® (avapritinib) and GAVRETO® (pralsetinib) across multiple indications and geographies, including the creation of commercial infrastructure and successful market access efforts in the U.S. and Europe. Prior to joining us, from January 2016 to October 2018, Ms. Rossi served as the Multiple Sclerosis business unit head, North America, at Sanofi Genzyme, a global business unit of Sanofi S.A. In this role, she was responsible for all aspects of the financial performance of Sanofi Genzyme’s multiple sclerosis franchise and increased market share for existing products, led the launch of new therapies and optimized operations to accelerate patient access. Previously, Ms. Rossi served as vice president, Multiple Sclerosis Sales at Sanofi Genzyme from May 2014 to December 2015 and vice president, Multiple Sclerosis Patient and Provider Services at Sanofi Genzyme from June 2012 to May 2014. Prior to joining Sanofi Genzyme, Ms. Rossi served in various roles at Biogen, Inc., or Biogen, including head, commercial strategy for Eidetica Biopharma GmbH, Biogen’s biosimilar-focused venture, and U.S. brand leader for TYSABRI® (natalizumab). In addition, Ms. Rossi consulted in the healthcare practice at the Boston Consulting Group. Ms. Rossi has served as a member of the board of directors of Xilio Therapeutics, Inc. since April 2021 and currently serves as a member of its audit committee and as chair of its compensation committee. Ms. Rossi holds a B.S. in biology, cum laude, from Duke University and an M.B.A. from Harvard Business School.

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Executive Compensation

COMPENSATION DISCUSSION AND ANALYSIS

Our compensation committee is responsible for reviewing and approving the compensation of our named executive officers, including base salary, cash and equity incentive compensation levels and plan designs, severance arrangements, change-in-control benefits and other forms of executive compensation. This committee is also responsible for evaluating our company’s performance against its goals and making related recommendations to our board of directors, assessing the performance of our named executive officers, and ensuring our compensation program is aligned with the objectives described below and competitive with those of other companies in our industry with which we vie for talent. This section discusses the principles underlying our compensation committee’s policies and decisions with respect to the compensation of our named executive officers.

For 2024, our named executive officers were as follows:

EXECUTIVE SUMMARY

We are a global, fully integrated biopharmaceutical company that invents life-changing medicines.  We seek to alleviate  human suffering by solving important medical problems in two core focus areas: allergy/inflammation and oncology/hematology. Our approach begins by targeting the root causes of disease, using deep scientific knowledge in our core focus areas and drug discovery expertise across multiple therapeutic modalities. We have a track record of success with two approved medicines, including AYVAKIT®/AYVAKYT® (avapritinib) which we are bringing to patients with SM in the U.S. and Europe. Leveraging our established research, development, and commercial capability and infrastructure, we now aim to significantly scale our impact by advancing a broad pipeline of programs ranging from early science to advanced clinical trials in mast cell diseases including SM and chronic urticaria, breast cancer and other solid tumors.

Since 2011, we have advanced a drug discovery approach that combines evolving biological insights with our proprietary research platform and drug design capabilities, with a focus on small molecule inhibitors and target protein degraders. We aim to rapidly and reproducibly translate science into a life-changing clinical benefit for broad populations of patients with significant medical needs. Our focused business model integrates our research engine with robust clinical development and commercial capabilities in allergy/inflammation and solid tumors to create a sustainable cycle of innovation.

Select 2024 Executive Highlights

In 2024, we made substantial progress in our mission to bring life-changing medicines to patients with allergic and inflammatory disorders and cancer. We achieved a number of significant milestones in 2024, including the following, toward our corporate goals described below in this Compensation Discussion and Analysis section.

Expand leadership in SM and drive topline revenue growth through the compliant delivery of AYVAKIT to patients globally.  

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Execute with quality and integrity, scaling our research and development pipeline to meet the needs of larger patient populations. 

Operate with financial discipline and organizational resilience, prioritizing pipeline, commercial and internal talent investment opportunities to achieve sustainable growth.  

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EXECUTIVE COMPENSATION OBJECTIVES AND PHILOSOPHY

Our compensation committee believes that the most effective compensation program is one that promotes company performance in order to reward value creation for stockholders and progress towards achieving our mission of delivering life-changing medicines to address unmet medical needs of our patients. The objectives of our compensation program are to:

To achieve its objectives, our compensation committee evaluates our executive compensation program with the goal of setting total compensation at levels that align with our total rewards strategy, size and company life stage. Specifically, below are the key elements targeted by our compensation committee for our 2024 executive compensation programs:

Base salary

As discussed below, in seeking to ensure that base salaries reflect each executive’s experience, performance and responsibility, our compensation committee applies judgment in establishing targeted pay levels, taking into account not only competitive market data, but also factors such as organizational and individual performance, scope of responsibility, critical needs and skill sets, leadership and succession planning. The committee believes the current base salaries for our named executive officers are competitive with the base salaries of other companies in our industry and region that compete with us for executive talent.

Annual performance-based cash incentive compensation

Our compensation program links a substantial portion of our named executive officers’ annual compensation to the achievement of pre-determined corporate and applicable individual performance goals as part of the annual executive bonus plan adopted by our board of directors, or the executive bonus plan. Those goals include: scientific, business, organizational and operational goals such as our commercialization activities; progress in our clinical trials and research programs; key research and development achievements; maintaining the strong financial health of the company, including implementation of appropriate financing strategies; maintaining and establishing key strategic relationships; sustaining and reinforcing our diverse and differentiated culture through retention and development of high-performing talent; and achievement of desired financial metrics. Our compensation committee general considers competitive compensation data from annual total compensation of peer companies to assist in making decisions on annual performance-based cash incentive compensation, and has imposed caps on executive bonus plan payouts at 150% of the target payout for individual performance. Based on competitive peer compensation data provided by, and the recommendation of, our compensation committee’s outside compensation consultant, our compensation committee decided that for performance years beginning with 2025, the maximum payout under the executive bonus plan for the corporate performance goal achievement is 200% of the target payout, while the individual goal achievement payout remains capped at 150%. This change aligns to the median maximum executive bonus payout opportunity among our peer companies, ensuring our incentive programs remain competitive with industry benchmarks and reinforces our pay-for-performance philosophy.

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Long-term equity incentive compensation

We provide a significant portion of our executive compensation in the form of stock options and RSUs that vest over time contingent upon continued service, which we believe helps to retain our executives and aligns their interests with those of our stockholders by allowing them to participate in the longer-term success of our company as reflected in the appreciation of our stock price. In 2023 we also introduced PSUs for all our executive officers and executive team members, which require both continued service and performance of our relative total stockholder return in order to vest, balancing both retention and stronger alignment with company performance and stockholder interests. When determining equity incentive compensation for our named executive officers, our compensation committee considers a host of factors in comparison to our peer group, including the following: annual long-term incentive target values, annual equity awards expressed as a percent of total shares outstanding, total annual and cumulative potential dilution, the retentive value of outstanding awards and total equity ownership, and the equity compensation practices and vehicles of other companies in

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our industry that compete with us for talent. Given the dynamic biopharmaceutical market, our compensation committee does not overemphasize any one of these perspectives. Rather, the compensation committee takes a holistic view, further considering the factors enumerated above, the achievement of our corporate and applicable individual goals and the impact on total stockholder return, when determining actual award levels for each of the named executive officers.

We believe that targeting and delivering overall compensation in this manner, including the strong emphasis on pay-for-performance and at-risk pay, are necessary and appropriate in order to attract and retain the quality of talent we need to successfully grow our business, achieve our goals, sustain strong performance, and seek to ensure that compensation levels are competitive with other companies with which we vie for talent. In addition, we believe this approach to overall compensation creates a strong alignment with stockholder value and encourages long-term value creation. However, any individual employee’s compensation may vary from the targeted pay framework, based on the unique responsibilities and requirements of the position, experience and other qualifications, internal parity relative to similar positions within the company, and individual or company performance relative to performance goals and our peer group to ensure appropriate pay-for-performance alignment. While we do not have a formal or informal policy for allocating between long-term and short-term compensation, between cash and non-cash compensation or among different forms of non-cash compensation, we generally strive to provide our named executive officers with a balance of short-term and long-term incentives to encourage consistently strong performance to help contribute sustained value over time.

For 2024, 94% of our chief executive officer’s and 88% of our other named executive officers’ target compensation was performance-based through their pre-determined annual performance goals (corporate goals for our chief executive officer and corporate and individual goals for our other named executive officers) tied to our executive bonus plan and long-term equity awards to incentivize performance to drive stock appreciation and, therefore, at-risk pay:

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* Based on 2024 annualized salary, bonus opportunity at target for 2024 performance, and grant date fair value of long-term equity incentive awards granted in 2024, all of which is averaged for our named executive officers other than our chief executive officer. Please note that the above excludes all other unspecified forms of compensation and therefore does not fully reflect the amounts included in the Summary Compensation Table.

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COMPENSATION ELEMENTS

Our compensation committee seeks to ensure that our compensation program is aligned with the interests of our stockholders and our business goals and that the total compensation paid to each of our named executive officers is fair, reasonable, competitive and reflective of the unique and critical skills, experience and knowledge that they bring to Blueprint. As described in more detail below, key elements of our compensation program include the following:

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In addition to our direct compensation elements, the following components of our compensation program are designed to align with stockholder interests and market best practices while being able to achieve our stated objectives and philosophy and support our ambitious business goals:

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ANNUAL SAY-ON-PAY VOTE ON EXECUTIVE COMPENSATION

The compensation committee considered the results of the non-binding stockholder advisory votes on the compensation of our named executive officers conducted at our 2024 annual meeting of stockholders, commonly referred to as a “say-on-pay” vote. As reported in our current report on Form 8-K, filed with the SEC on June 14, 2024, or the June 2024 8-K, approximately 98% of the votes cast on the proposal expressed support for the compensation program offered to our named executive officers as disclosed in last year’s proxy statement. The compensation committee appreciates this support and believes it indicates that our stockholders are supportive of our current executive compensation structure and policies. As such, the compensation committee made no changes to our 2024 executive compensation program as a result of the say-on-pay vote.

Further, our board of directors conducts the non-binding advisory say-on-pay vote annually, thereby giving our stockholders the opportunity to provide feedback on the compensation of our named executive officers each year. As reported in the June 2024 8-K, approximately 99% of the votes cast on the proposal regarding the frequency of say-on-pay expressed support for an annual advisory vote on the compensation paid to our named executive officers. Our board of directors and our compensation committee will consider the outcome of the say-on-pay vote, as well as feedback received throughout the year, when making compensation decisions for our named executive officers in the future.

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OVERVIEW OF EXECUTIVE COMPENSATION PROCESS

ROLE OF THE COMPENSATION COMMITTEE

The compensation committee works closely with Aon’s Human Capital Solutions practice, a division of Aon plc, or Aon (formerly known as Radford), throughout the year to develop our executive compensation program and to align pay with performance, stockholder interests, and pay at our peer companies. Annualized base salaries and annual performance-based cash incentives and equity incentive awards for all employees, including our named executive officers, are generally determined in the first quarter of the year based on company and individual performance in the prior year, as well as other factors, including compensation trends in the biopharmaceutical industry and among our benchmark peers.

Our compensation committee has delegated authority to our chief executive officer to grant equity awards under our 2024 Plan, and prior to its adoption, under the 2015 Plan, to certain employees of the company or any of its affiliates in connection with hiring, promotions (other than those that occur as part of our annual performance and compensation review process), and employee recognition or exceptional performance, in each case, subject to certain limitations. In particular, our chief executive officer is not authorized to grant equity awards to: (i) an employee who is a member of our executive team; (ii) an employee who is subject to Section 16 of the Exchange Act; (iii) the chief executive officer; or (iv) any other person whom our board of directors or compensation committee, respectively, may from time to time designate in writing as not being eligible to receive equity awards under the authority delegated to the chief executive officer. In addition, the number of shares underlying any equity awards granted by our chief executive officer must be within the range specified by our compensation committee for these awards, and the aggregate number of shares underlying equity awards that our chief executive officer may grant in any one calendar year or to any person in any one calendar year must be within specified limits established by our compensation committee. The exercise price of stock options must be equal to the closing price of our common stock on the Nasdaq Global Select Market on the date of grant, and all equity awards must have vesting terms consistent with those set forth in our standard equity award agreements as previously approved by our compensation committee. In addition, our chief executive officer is required to maintain a list of equity awards granted pursuant to such delegated authority and periodically report to our compensation committee regarding such awards.

With respect to any equity awards granted by our chief executive officer to new hires, our chief executive officer approves the awards in connection with such hires which are generally to be granted on the first day of the first or second calendar month following the date of such new hires’ first date of employment, depending upon where that start date falls within the month. With respect to any equity awards granted by our chief executive officer to employees in connection with mid-year promotions, our chief executive officer approves the awards in connection with such promotions and typically provides that the awards are to be granted on July 1 of the applicable year. If circumstances arise that would warrant a grant of an equity award other than at the times set forth above, the compensation committee or board may consider and approve such grants.

Notwithstanding the delegation of authority to our chief executive officer to grant equity awards in connection with certain new hires and promotions, our compensation committee approves all equity awards that are typically granted in the first quarter, in connection with our annual performance and compensation review process and those for which the compensation committee has not delegated granting authority to our chief executive officer. Prior to the adoption of the 2024 Plan, the compensation committee approved all equity grants that were granted under our 2020 Plan. Since the adoption of the 2024 Plan in June 2024, the 2020 Plan and 2015 Plan were retired and we ceased issuing new awards under the 2020 Plan and 2015 Plan.

ROLE OF MANAGEMENT

Our chief executive officer makes performance and compensation recommendations to our compensation committee for our other executive officers, including our named executive officers. Our chief executive officer’s performance is evaluated and approved directly by the compensation committee, considering input from our board of directors. Evaluations of each of our executive officers are based on our overall corporate performance against the annual goals approved by the board of directors at the beginning of each year and, in the case of executive officers other than our chief executive officer, the achievement of individual goals, as discussed in more detail

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below. The evaluation of our chief executive officer is based solely on our corporate performance goals, in recognition of her overall responsibility for our corporate performance and to incentivize the chief executive officer to drive the execution of our strategic plans and achievement of our corporate goals.

ROLE OF THE COMPENSATION CONSULTANT

The compensation committee has the sole authority to retain, at our expense, one or more third-party compensation consultants to assist it in performing its responsibilities. The compensation committee may terminate the services of the consultant if the compensation committee deems it appropriate. In 2024, the compensation committee utilized the services of Aon to assist it in fulfilling its responsibilities. Aon was retained exclusively by the compensation committee and has not been retained by management to perform any additional work for the company other than projects performed at the direction of the compensation committee. Aon provides analysis and recommendations regarding:

Aon advises the compensation committee on all of the principal aspects of executive and director compensation, including executive new hire compensation arrangements. Upon request, Aon consultants attend meetings of the compensation committee, including executive sessions in which executive compensation issues are discussed. In addition, we subscribe to Aon’s various global annual and specialized life sciences and general industry compensation surveys on an ongoing basis. At the end of 2024, Aon’s broad based compensation consulting services provided additional support to our internal human resources team to support our year-end compensation process for our broader employee population below the executive team and excluding our board of directors. Aon reports to the compensation committee and not to management, although it meets with management for purposes of gathering information for its analyses and recommendations. The compensation committee annually evaluates its engagement of compensation consultants, and selected Aon to advise with respect to compensation matters based on Aon’s industry experience and reputation, which our compensation committee concluded continues to give Aon useful context and knowledge to advise it. The compensation committee has assessed the independence of Aon pursuant to SEC and Nasdaq Listing Rules and concluded that no conflict of interest exists that would prevent Aon from independently advising the compensation committee.

DEFINING AND COMPARING COMPENSATION TO MARKET BENCHMARKS

In evaluating the total compensation of our named executive officers, our compensation committee, using information provided by Aon, establishes a peer group of publicly traded companies in the biopharmaceutical and biotechnology industries that is selected based on a balance of the following criteria, of public companies:

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Based on these criteria, our peer group for 2024 compensation setting, referred to as our 2024 peer group, as approved by our compensation committee, comprised the following 17 companies:

* Addition to 2024 peer group from the 2023 peer group; removed Alnylam Pharmaceuticals, Inc. and United Therapeutics, Inc.

The compensation committee believes the compensation practices of our 2024 peer group provide us with appropriate benchmarks for evaluating the compensation of our named executive officers. Such information provides useful context as well as a solid reference point for making decisions. Notwithstanding the similarities of our 2024 peer group to our company, due to the nature of our business, we compete for executive talent with many companies that are larger and more established than we are or that possess greater resources than we do, as well as with prestigious academic and non-profit institutions. Other considerations, including market factors, the experience level of the executive and the executive’s performance against established corporate goals and individual objectives, may require that our compensation committee vary from its compensation practices or general compensation philosophy under certain circumstances.

For purposes of determining our peer group for 2024 compensation comparisons, our compensation committee, with the advice of Aon, examined our 2023 peer group in light of our continued growth throughout 2023 and into 2024, with reference to market capitalization, therapeutic area, stage of development, number of employees and other key business metrics, as well as whether the companies in our 2023 peer group suffered any clinical setbacks or experienced reduced growth or had been acquired. Based on these considerations, to determine our 2024 peer group, our compensation committee added the following two companies to our 2024 peer group – Deciphera Pharmaceuticals, Inc. and PTC Therapeutics, Inc. – and removed the following two companies that had been included in our 2023 peer group – Alnylam Pharmaceuticals, Inc. and United Therapeutics Corporation.

EXECUTIVE COMPENSATION ELEMENTS

As previously discussed above, the primary elements of our executive compensation program are base salary, annual performance-based cash incentives and long-term equity incentive awards. Our compensation committee uses sound judgment to allocate long-term and short-term compensation for our named executive officers, in alignment with our pay-for-performance philosophy and the long-term interests of stockholders. After reviewing information provided by Aon and other relevant data, our compensation committee exercises its judgment to determine what it believes to be the appropriate level and mix of the various compensation components. We generally strive to provide our named executive officers with a balance of short-term and long-term incentives to encourage consistently strong performance in alignment with delivering value to our stockholders. For more information, please see “Executive Compensation—Compensation Objectives and Philosophy.”

In addition, we provide our executives with benefits that are available to all employees, including medical, vision and dental insurance; life and disability insurance; medical and dependent care flexible spending accounts; a 401(k) plan; and an opportunity to invest in our company pursuant to our 2015 Employee Stock Purchase Plan, or 2015 ESPP. We offer our executives severance benefits upon an involuntary or constructive termination, as we believe such post-employment compensation protections are appropriate in light of similar benefits available to executive officers at companies in our peer group. We also offer our executives enhanced severance benefits in connection with a double-trigger termination, or an involuntary or constructive termination after a change-in-control. We believe that reasonable and competitive change-in-control payments and benefits are an important part of an

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executive compensation program to attract and retain senior executives. We also believe such payments and benefits are in the best interests of our stockholders because they incentivize senior executives to continue to strive to achieve stockholder value in connection with change-in-control situations, particularly where the possibility of a change-in-control and the related uncertainty may lead to the departure or distraction of senior executives to the detriment of our company and our stockholders.

BASE SALARY

We use base salaries to recognize the experience, skills, knowledge and responsibilities required of all our employees, including our named executive officers. None of our named executive officers is currently party to an employment agreement or other agreement or arrangement that provides for automatic or scheduled increases in base salary. However, on an annual basis, our compensation committee reviews and evaluates, with input from our chief executive officer and our compensation consultant, the need for adjustment of the base salaries of our executive officers (other than our chief executive officer), and our compensation committee reviews and evaluates, without input from our chief executive officer and with input from our compensation consultant, the need for adjustment of the base salary of our chief executive officer, in each case, based on among other things, changes and expected changes in the scope of an executive officer’s responsibilities, whether or not due to a promotion, the individual contributions made by and performance of the executive officer during the prior year, the unique skills and experience of the executive officer, our overall growth and development as a company and general salary or other market trends among companies in our peer group or in our industry.

In February 2024, our compensation committee approved salary increases for each of our named executive officers, effective January 1, 2024, based on a review of market data provided by Aon, the compensation levels of our named executive officers, the company’s performance against our 2023 corporate performance goals and, in the case of executive officers other than our chief executive officer, each executive officer’s achievement of individual goals. The table below sets forth the adjustments to annualized base salary, in dollars and as a percentage, for each of our named executive officers: