UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 2)*

ACCELERON PHARMA INC.

(Name of Issuer)

Common Stock, $0.001 par value

(Title of Class of Securities)

00434H108

(CUSIP Number)

Polaris Partners

1000 Winter Street, Suite 3350

Waltham, MA 02451

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

May 5, 2014

(Date of Event which Requires Filing of this Statement)

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 §§240.13d-1(e), 240.13d-1(f) or 240.13d-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 information required on 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 (“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).

This Amendment No. 2 (this “Amendment No. 2”) amends and supplements the Schedule 13D originally filed with the Securities and Exchange Commission (the “SEC”) on February 14, 2014, by the Reporting Persons, as amended by Amendment No. 1 (“Amendment No. 1”) filed with the SEC on April 7, 2014 (the “Schedule 13D”), with respect to shares of common stock, par value $0.001 per share of the Issuer (“Common Stock”) beneficially owned by the Reporting Persons. Except as amended or supplemented in this Amendment No. 2, all other information in the Schedule 13D is as set forth therein. Capitalized terms used herein but not defined shall have the meanings ascribed thereto in the Schedule 13D.

Item 5. Interest in Securities of the Issuer.

Item 5 of the Schedule 13D is hereby amended and restated in its entirety as follows:

(a) and (b).

Item 6. Contracts, Arrangements, Understandings or Relationships With Respect to Securities of the Issuer.

Item 6 of the Schedule 13D is hereby amended and restated in its entirety as follows:

On April 2, 2014, PVP IV and PVPE IV entered into a Stock Purchase Agreement with Celgene Corporation, a Delaware corporation (“Celgene”), pursuant to which PVP IV and PVPE IV agreed to sell 307,893 and 5,598 shares of Common Stock, respectively, of the Issuer held by PVP IV and PVPE IV to Celgene for a purchase price of $42.86 per share (the “Transaction”).

The Transaction was subject to customary closing conditions, including expiration of the applicable waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976, as amended, in the United States. The Transaction closed on May 5, 2014.

The Stock Purchase Agreement is attached to Amendment No. 1 as Exhibit 99.1, and the information set forth in response to this Item 6 is qualified in its entirety by reference to the Stock Purchase Agreement which is incorporated by reference herein.

Item 7. Material to be Filed as Exhibits.

Exhibit 1—Joint Filing Agreement

Exhibit 2—Power of Attorney, dated June 15, 2011, signed by Jonathan A. Flint and Terrance G. McGuire, in their respective capacities as managing members of Polaris Venture Management Co. IV, L.L.C.

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.

Date: May 12, 2014

Exhibit 1

JOINT FILING AGREEMENT PURSUANT TO RULE 13d-1(k)(1)

The undersigned acknowledge and agree that the foregoing statement on Schedule 13D is filed on behalf of each of the undersigned and that all subsequent amendments to this statement on Schedule 13D shall be filed on behalf of each of the undersigned without the necessity of filing additional joint filing statements. The undersigned acknowledge that each shall be responsible for the timely filing of such amendments, and for the completeness and accuracy of the information concerning him, her or it contained herein, but shall not be responsible for the completeness and accuracy of the information concerning the other entities or persons, except to the extent that he, she or it knows or has reason to believe that such information is inaccurate.

Date: May 12, 2014

Exhibit 2

POLARIS VENTURE MANAGEMENT CO. L.L.C.

POLARIS VENTURE MANAGEMENT CO. II, L.L.C.

POLARIS VENTURE MANAGEMENT CO. III, L.L.C.

POLARIS VENTURE MANAGEMENT CO. IV, L.L.C.

POLARIS VENTURE MANAGEMENT CO. V, L.L.C.

POLARIS VENTURE MANAGEMENT CO. VI, L.L.C.

NORTH STAR VENTURE MANAGEMENT, INC.

NORTH STAR VENTURE MANAGEMENT 2000, L.L.C.

NORTH STAR VENTURE MANAGEMENT 2010, L.L.C.

NORTH STAR VENTURE MANAGEMENT AVIATION, L.L.C.

POWER OF ATTORNEY

Each of the undersigned, including (i) Polaris Venture Management Co. VI, L.L.C., a Delaware limited liability company, in the normal course of its business and in its capacity as the general partner of Polaris Venture Partners VI, L.P., a Delaware limited partnership, and Polaris Venture Partners Founders’ Fund VI, L.P., a Delaware limited partnership, (ii) Polaris Venture Management Co. V, L.L.C., a Delaware limited liability company, in the normal course of its business and in its capacity as the general partner of Polaris Venture Partners V, L.P., a Delaware limited partnership, Polaris Venture Partners Entrepreneur’s Fund V, L.P., a Delaware limited partnership, and Polaris Venture Partners Founders’ Fund V, L.P., a Delaware limited partnership, (iii) Polaris Venture Management IV, L.L.C., a Delaware limited liability company, in the normal course of its business and its capacity as the general partner of Polaris Venture Partners IV, L.P., a Delaware limited partnership, and Polaris Venture Partners Founders’ Fund IV, L.P., a Delaware limited partnership, (iv) Polaris Venture Management Co. III, L.L.C., a Delaware limited liability company, in the normal course of its business and in its capacity as the general partner of Polaris Venture Partners III, L.P., a Delaware limited partnership, Polaris Venture Partners Entrepreneurs’ Fund III, L.P., a Delaware limited partnership, and Polaris Venture Partners Founders’ Fund III, L.P., a Delaware limited partnership, (v) Polaris Venture Management Co. II, L.L.C., a Delaware limited liability company, in the normal course of its business and in its capacity as the general partner of Polaris Venture Partners II, L.P., a Delaware limited partnership, and Polaris Venture Partners Founders’ Fund II, L.P., a Delaware limited partnership, (vi) Polaris Venture Management Co., L.L.C., a Delaware limited liability company, in the normal course of its business and in its capacity as the general partner of Polaris Venture Partners, L.P., a Delaware limited partnership and Polaris Venture Partners Founders’ Fund, L.P., a Delaware limited partnership, (vii) North Star Venture Management 2000, L.L.C., a Delaware limited liability company, in the normal course of its business and in its capacity as the sole member of North Star Venture Management Aviation, L.L.C., a Delaware limited liability company, (viii) North Star Venture Management 2010, L.L.C., a Delaware limited liability company, in the normal course of its business and in its capacity as the sole member of North Star Venture Management Aviation, L.L.C., a Delaware limited liability company, (ix) North Star Venture Management, Inc., a Delaware close corporation, in the normal course of its business, and (x) Jonathan A. Flint and Terrance C. McGuire in their capacity as managers of North Star Venture Management Aviation, L.L.C., a Delaware limited liability company, hereby constitutes and approves John Gannon as its true and lawful attorney-in-fact to:

The undersigned hereby grants to such attorney-in-fact full power and authority to do and perform all and every act and thing whatsoever requisite, necessary, and proper to be done in the exercise of any of the rights and powers herein granted, as fully to all intents and purposes as the undersigned might or could do if personally present, with full power of substitution or revocation, hereby ratifying and confirming all that each such attorney-in-fact, or his substitute or substitutes, shall lawfully do or cause to be done by virtue of this Power of Attorney and the right and powers herein granted. The undersigned acknowledges that no such attorney-in-fact, in serving in such capacity at the request of the undersigned, is hereby assuming any of the undersigned’s responsibilities under the laws of the United States or any state. This Power of Attorney shall remain in full force and effect from the date hereof until revoked by the undersigned in a signed writing delivered to the foregoing attorney-in-fact.

[SIGNATURE PAGES FOLLOW]

2

IN WITNESS WHEREOF, each of the undersigned has caused this Power of Attorney to be executed effective as of June 15, 2011.

IN WITNESS WHEREOF, each of the undersigned has caused this Power of Attorney to be executed effective as of June 15, 2011.