SCHEDULE 13D/A 0001104659-23-083070 0001802528 XXXXXXXX LIVE 3 Common Stock, $0.00001 par value 10/10/2025 false 0001974640 03770N101 Apogee Therapeutics, Inc.

221 Crescent Street Building 17, Suite 102b Waltham MA 02453

Ms. Erin O'Connor (267) 262-5300 Fairmount Funds Management LLC 200 Barr Harbor Drive, Suite 400 West Conshohocken PA 19428 0001802528 N Fairmount Funds Management LLC a AF N DE 0.00 5678239.00 0.00 5678239.00 5678239.00 N 9.81 IA The securities include (i) 2,048,647 shares of common stock, $0.00001 par value per share (the "Common Stock") and (ii) 3,629,592 shares of Common Stock issuable upon conversion of 3,629,592 shares of Non-Voting Common Stock, par value $0.00001 per share (the "Non-Voting Common Stock"), the conversion of which is subject to a beneficial ownership limitation of 9.99% of the outstanding Common Stock, both directly held by Fairmount Healthcare Fund II L.P., a Delaware limited partnership ("Fund II"). The securities exclude shares of Common Stock issuable upon conversion of shares of Non-Voting Common Stock held by Fund II in excess of the beneficial ownership limitation. Row 13 is based on 57,863,578 shares of Common Stock outstanding as of October 10, 2025, consisting of (i) 54,149,570 shares of Common Stock outstanding as of October 10, 2025, as reported in the Company's final prospectus supplement filed pursuant to Rule 424(b)(5) dated October 8, 2025, (ii) 84,416 shares underlying vested stock options owned by the Reporting Persons and (iii) 3,629,592 shares of Common Stock underlying the 3,629,592 shares of Non-Voting Common Stock owned by Fund II, applying the beneficial ownership limitation. 0001769651 N Fairmount Healthcare Fund II L.P. a AF N DE 0.00 5678239.00 0.00 5678239.00 5678239.00 N 9.81 PN The securities include (i) 2,048,647 shares of Common Stock and (ii) 3,629,592 shares of Common Stock issuable upon conversion of 3,629,592 shares of Non-Voting Common Stock, the conversion of which is subject to a beneficial ownership limitation of 9.99% of the outstanding Common Stock, both directly held by Fund II. The securities exclude shares of Common Stock issuable upon conversion of shares of Non-Voting Common Stock held by Fund II in excess of the beneficial ownership limitation. Row 13 is based on 57,863,578 shares of Common Stock outstanding as of October 10, 2025, consisting of (i) 54,149,570 shares of Common Stock outstanding as of October 10, 2025, as reported in the Company's final prospectus supplement filed pursuant to Rule 424(b)(5) dated October 8, 2025, (ii) 84,416 shares underlying vested stock options owned by the Reporting Persons and (iii) 3,629,592 shares of Common Stock underlying the 3,629,592 shares of Non-Voting Common Stock owned by Fund II, applying the beneficial ownership limitation. 0001663607 N Peter Evan Harwin a AF N X1 93374.00 5683507.00 93374.00 5683507.00 5776881.00 N 9.99 IN The securities include (a) 51,166 shares of Common Stock held directly by Mr. Harwin, (b) 42,208 shares of Common Stock underlying vested options held by Mr. Harwin* and (c) Fund II's direct holdings of (i) 2,048,647 shares of Common Stock and (ii) 3,634,860 shares of Common Stock issuable upon conversion of 3,634,860 shares of Non-Voting Common Stock, the conversion of which is subject to a beneficial ownership limitation of 9.99% of the outstanding Common Stock. The securities exclude shares of Common Stock issuable upon conversion of shares of Non-Voting Common Stock in excess of the beneficial ownership limitation. Row 13 is based on 57,826,638 shares of Common Stock outstanding as of October 10, 2025, consisting of (i) 54,149,570 shares of Common Stock outstanding as of October 10, 2025, as reported in the Company's final prospectus supplement filed pursuant to Rule 424(b)(5) dated October 8, 2025, (ii) 42,208 shares of Common Stock underlying vested options held by Mr. Harwin and (iii) 3,634,860 shares of Common Stock underlying the 3,634,860 shares of Non-Voting Common Stock owned by Fund II, subject to the beneficial ownership limitation. * Under Mr. Harwin's arrangement with Fairmount, Mr. Harwin holds the options for one or more investment vehicles managed by Fairmount (each, a "Fairmount Fund"). Mr. Harwin is obligated to turn over to Fairmount any net cash or stock received from the option for the benefit of such Fairmount Fund. Mr. Harwin therefore disclaims beneficial ownership of the option and underlying common stock. 0001830177 N Tomas Kiselak a AF N 2B 93374.00 5683507.00 93374.00 5683507.00 5776881.00 N 9.99 IN The securities include (a) 51,166 shares of Common Stock held directly by Mr. Kiselak, (b) 42,208 shares of Common Stock underlying vested options held by Mr. Kiselak* and (c) Fund II's direct holdings of (i) 2,048,647 shares of Common Stock and (ii) 3,634,860 shares of Common Stock issuable upon conversion of 3,634,860 shares of Non-Voting Common Stock, the conversion of which is subject to a beneficial ownership limitation of 9.99% of the outstanding Common Stock. The securities exclude shares of Common Stock issuable upon conversion of shares of Non-Voting Common Stock in excess of the beneficial ownership limitation. Row 13 is based on 57,826,638 shares of Common Stock outstanding as of October 10, 2025, consisting of (i) 54,149,570 shares of Common Stock outstanding as of October 10, 2025, as reported in the Company's final prospectus supplement filed pursuant to Rule 424(b)(5) dated October 8, 2025, (ii) 42,208 shares of Common Stock underlying vested options held by Mr. Kiselak and (iii) 3,634,860 shares of Common Stock underlying the 3,634,860 shares of Non-Voting Common Stock owned by Fund II, subject to the beneficial ownership limitation. * Under Mr. Kiselak's arrangement with Fairmount, Mr. Kiselak holds the options for one or more investment vehicles managed by Fairmount (each, a "Fairmount Fund"). Mr. Kiselak is obligated to turn over to Fairmount any net cash or stock received from the option for the benefit of such Fairmount Fund. Mr. Kiselak therefore disclaims beneficial ownership of the option and underlying common stock. Common Stock, $0.00001 par value Apogee Therapeutics, Inc. 221 Crescent Street Building 17, Suite 102b Waltham MA 02453 This Amendment No. 3 amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on July 21,2023, Amendment No. 1 filed on January 31, 2024 and Amendment No. 2 filed on April 1, 2024 (as amended, the "Statement" or the "Schedule 13D") by the Reporting Persons with respect to the Common Stock of the Company. Unless otherwise defined herein, capitalized terms used in this Amendment No. 3 shall have the meanings ascribed to them in the Statement. Unless amended or supplemented below, the information in the Statement remains unchanged. This Amendment No. 3 is being filed solely to report the Reporting Persons' entry into a lock-agreement with the Company in connection with the Company's underwritten public offering; the number of shares of Common Stock and Non-Voting Common Stock beneficially owned by the Reporting Persons has not changed since Amendment No. 2 to the Statement, filed on April 1, 2024. Item 2(a) of the Statement is hereby amended in its entirety as follows: This Schedule 13D is being filed jointly by (1) Fairmount; (2) Fund II; (3) Peter Harwin; and (4) Tomas Kiselak (Fairmount, Fund II, Mr. Harwin, and Mr. Kiselak are collectively referred to herein as the "Reporting Persons"). The joint filing agreement of the Reporting Persons is attached as Exhibit 99.1 to this Schedule 13D. Fairmount serves as investment manager for Fund II and may be deemed a beneficial owner, for purposes of Section 13(d) of the Securities Exchange Act of 1934 (the "Act"), of any securities of the Company held by Fund II. Fund II has delegated to Fairmount the sole power to vote and the sole power to dispose of all securities held in Fund II's portfolio, including the shares of Common Stock reported herein. Because Fund II has divested itself of voting and investment power over the reported securities it holds and may not revoke that delegation on less than 61 days' notice, Fund II disclaims beneficial ownership of the securities it holds for purposes of Section 13(d) of the Act and therefore disclaim any obligation to report ownership of the reported securities under Section 13(d) of the Act. As managers of Fairmount, Mr. Harwin and Mr. Kiselak may be deemed beneficial owners, for purposes of Section 13(d) of the Act, of any securities of the Company beneficially owned by Fairmount. Fairmount, Mr. Harwin and Mr. Kiselak disclaim beneficial ownership of the securities reported in this Schedule 13D other than for the purpose of determining their obligations under Section 13(d) of the Act, and the filing of this Schedule 13D shall not be deemed an admission that any of Fairmount, Mr. Harwin or Mr. Kiselak is the beneficial owner of such securities for any other purpose. Item 2(c) of the Statement is hereby amended in its entirety as follows: The principal business of Fairmount is to provide discretionary investment management services to qualified investors through Fund II, a private pooled investment vehicle. The principal occupation of Mr. Harwin and Mr. Kiselak is investment management. The information in rows 11 and 13 of each of the cover pages (including the explanatory note in the "Comments") of this Amendment No. 1 is incorporated by reference herein. The information in rows 7 through 10 of each of the cover pages of this Amendment No. 3 is incorporated by reference herein. None Fairmount is the investment manager to Fund II has voting and dispositive power over shares of Common Stock held on behalf of Fund II. Lock-Up Agreement In connection with the Company's underwritten public offering of common stock and pre-funded warrants that closed on October 10, 2025, the Fund II entered into a customary lock-up letter agreement (the "Lock-Up Agreement") with Jefferies LLC, as representative of the several underwriters party to an underwriting agreement with the Company. Pursuant to the Lock-Up Agreement, Fund II agreed to refrain from selling shares of the Company's securities without the consent of Jefferies LLC, and other customary lock-up conditions, for a period of 60 days from the date of the Company's final prospectus supplement related to the offering. The Reporting Persons did not purchase any securities of the Company or otherwise participate in the offering. The foregoing description of the Lock-Up Agreement does not purport to be complete and is qualified in its entirety by reference to the form of the Lock-Up Agreement, which is filed as Exhibit 99.2 to this Schedule 13D and incorporated herein by reference. 99.1 Joint Filing Agreement 99.2 Lock-Up Agreement (incorporated by reference to Exhibit A to the Underwriting Agreement filed as Exhibit 1.1 of the Company's Form 8-K filed with the SEC on October 10, 2025). Fairmount Funds Management LLC /s/ Peter Harwin 10/14/2025 /s/ Tomas Kiselak 10/14/2025 Fairmount Healthcare Fund II L.P. /s/ Peter Harwin 10/14/2025 /s/ Tomas Kiselak 10/14/2025 Peter Evan Harwin /s/ Peter Harwin 10/14/2025 Tomas Kiselak /s/ Tomas Kiselak 10/14/2025