UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.            )*

Lake Shore Bancorp, Inc.

Common Stock, $0.01 par value

510700 10 7

Rachel A. Foley

Chief Financial Officer

125 East Fourth Street

Dunkirk, NY 14048-2226

(716) 366-4070

April 3, 2006

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f) or 13d-1(g), check the following box: ¨

Note. Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See §240.13d-7 for other parties to whom copies are to be sent.

^*The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter the disclosures provided in a prior cover page.

The information required in the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (the “Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

SCHEDULE 13D

The securities as to which this Schedule 13D (the “Schedule”) relates are shares of common stock, par value $0.01 per share (the “Common Stock”), of Lake Shore Bancorp, Inc., a federal corporation (the “Company”), whose principal executive office is located at 125 East Fourth Street Dunkirk, New York 14048.

(a-c) This Schedule 13D is being filed by Lake Shore, MHC, a federally-chartered mutual holding company (the “MHC”). The MHC’s principal business is holding 55.0% of the Common Stock of the Company. The business address of the MHC is 125 East Fourth Street Dunkirk, New York 14048.

The following information is being provided with respect to each executive officer and director of the MHC (the “Insiders”).

(d) During the past five years, neither the MHC nor any of the Insiders has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

(e) During the past five years, neither the MHC nor any of the Insiders has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

(f) All of the Insiders are U.S. citizens. The MHC is a federal corporation.

On April 3, 2006, Lake Shore Savings and Loan Association (the “Bank) reorganized from the mutual to mutual holding company structure in accordance with the Plan of Reorganization and Minority Stock Issuance, as amended and restated (the “Plan”). Pursuant to the Plan, the Bank converted to stock form and the Company and the MHC were established. In connection with the reorganization, the Issuer issued a total of 6,612,500 shares of Common Stock of which 3,636,875 shares were issued to the MHC in exchange for the MHC’s ownership of 100% of the Bank’s common stock. All purchases by Insiders were from personal funds.

The reorganization will afford the Bank greater operating flexibility to meet current and future business goals. The mutual holding company corporate structure will better position the Bank to compete with other financial institutions and to take advantage of business opportunities. By issuing only a minority of Company’s common stock to the public, the organization preserves its ability to remain an independent community-oriented organization.

Although the MHC and Insiders intend to exercise their rights as stockholders, they do not currently have any plans or proposals which relate to or would result in: (a) the acquisition by any person of additional securities of the Company, or the disposition of securities of the Company; (b) an extraordinary corporate transaction, such as merger, reorganization or liquidation, involving the Company or any of its subsidiaries; (c) a sale or transfer of a material amount of assets of the Company or any of its subsidiaries; (d) any change in the present board of directors or management of the Company, including any plans or proposals to change the number or terms of directors or to fill any vacancies on the board; (e) any material change in the present capitalization or dividend policy of the Company; (f) any other material change in the Company’s business or corporate structure; (g) any change in the Company’s charter, by-laws, or

other instruments corresponding thereto or other actions which may impede the acquisition of control of the Company by any person; (h) causing a class of securities of the Company to be delisted from a national securities exchange or to cease to be authorized to be quoted in an inter-dealer quotation system or a registered national securities association; (i) a class of equity securities of the Company becoming eligible for termination of registration pursuant to Section 12(g)(4) of the Securities Exchange Act of 1934, as amended; or (j) any action similar to any of those enumerated above.

(a-b) The MHC beneficially owns (with sole voting and dispositive power) an aggregate of 3,636,875 shares of Common Stock or 55.0% of the 6,612,500 shares of Common Stock issued and outstanding on April 3, 2006. The Insiders individually have the sole power to vote and the sole power to dispose of the shares of Common Stock owned by them, except as otherwise indicated. The following information is provided with respect to the Insiders as of April 3, 2006:

(c) Not applicable.

(d) No person or entity other than the MHC has the right to receive, or the power to direct the receipt of dividends from, or the proceeds from the sale of the shares of the MHC’s Common Stock reported in this schedule.

(e) Not applicable.

As of the date of this Schedule 13D, neither the MHC nor any of the Insiders is a party to any contract, arrangement, understanding or relationship (legal or otherwise) among themselves or with any other person or persons with respect to the Common Stock, including but not limited to transfer or voting of any of the Common Stock, finder’s fees, joint ventures, loan or option arrangements, put or calls, guarantees of profits, division of profits or loss, the giving or withholding of proxies or otherwise subject to a contingency the occurrence of which would give another person voting or investment power over the Common Stock.

None.

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

April 13, 2006