UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 3)*

Agios Pharmaceuticals, Inc.

(Name of Issuer)

Common Stock, $0.0001 par value

(Title of Class of Securities)

00847X104

(CUSIP Number)

Mark J. Alles

Chief Executive Officer

Celgene Corporation

86 Morris Avenue

Summit, New Jersey 07901

(908) 673-9000

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

April 24, 2017

(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 which 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:  ¨

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). 

SCHEDULE 13D

SCHEDULE 13D

SCHEDULE 13D

SCHEDULE 13D

This Amendment No. 3 amends the Schedule 13D (the “Schedule 13D”) filed with the Securities and Exchange Commission (the “Commission”) on August 6, 2013 by Celgene European Investment Company LLC, Celgene Alpine Investment Co., LLC (“Celgene Alpine”) and Celgene Corporation (“Celgene”), as amended by Amendment No. 1 thereto filed with the Commission on April 30, 2014, and as amended by Amendment No. 2 thereto filed with the Commission on December 17, 2014, with respect to common stock, par value $0.0001 per share (“Common Stock”), of Agios Pharmaceuticals, Inc., a Delaware corporation (“Agios”). Capitalized terms used, but not defined herein, have the meanings ascribed to them in the Schedule 13D.

No modification.

Item 2 is hereby amended and supplemented by adding the Schedule A hereto. During the past five years, none of the Reporting Persons, nor, to the knowledge of the Reporting Persons, any of the persons listed on Schedule A hereto, has been (i) convicted in a criminal proceeding (excluding traffic violations and similar misdemeanors), or (ii) 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.

No modification.

Item 4 is hereby amended and supplemented by adding the following:

On April 24, 2017, Agios completed its underwritten public offering (the “Offering”) of 5,050,505 shares of Common Stock at a public offering price of $49.50 per share, and Celgene Switzerland LLC (“Celgene Switzerland”), a wholly-owned subsidiary of Celgene, purchased (the “Purchase”) 624,575 shares of Common Stock at a purchase price of $49.50 per share in the Offering for investment purposes. Following the Offering and the Purchase, Celgene Switzerland beneficially owns 624,575 shares of Common Stock and Celgene shares beneficial ownership of an aggregate of 5,867,279 shares of Common Stock, collectively representing approximately 12.4% of the shares of Common Stock outstanding as of April 24, 2017, which includes (a) 42,220,444 shares of Common Stock outstanding as of December 31, 2016, as reported by Agios in its prospectus filed with the Commission on April 19, 2017, and (b) 5,050,505 shares of Common Stock issued by Agios in the Offering.

Item 5(a)-(c) is hereby amended and restated as follows:

On April 24, 2017, Agios completed the Offering and Celgene Switzerland completed the Purchase. Following the Offering and the Purchase, Celgene Switzerland beneficially owns 624,575 shares of Common Stock and Celgene shares beneficial ownership of an aggregate of 5,867,279 shares of Common Stock, collectively representing approximately 12.4% of the shares of Common Stock outstanding as of April 24, 2017, which includes (a) 42,220,444 shares of Common Stock outstanding as of December 31, 2016, as reported by Agios in its prospectus filed with the Commission on April 19, 2017, and (b) 5,050,505 shares of Common Stock issued by Agios in the Offering.

No modification.

No modification.

SIGNATURE

After reasonable inquiry and to the best of its knowledge and belief, the undersigned certifies that the information set forth in this statement is true, complete and correct.

SCHEDULE A

Name, business address, present principal occupation or employment and place of citizenship of the directors and executive officers of the Reporting Persons

The name, business address and present principal occupation or employment of each of the directors and executive officers of the Reporting Persons are set forth below. The business address of each director and executive officer is c/o 86 Morris Avenue, Summit, New Jersey 07901. Unless otherwise indicated, each director and executive officer is a citizen of the United States.

CELGENE CORPORATION — BOARD OF DIRECTORS

CELGENE CORPORATION — EXECUTIVE OFFICERS

CELGENE SWITZERLAND LLC

CELGENE EUROPEAN INVESTMENT COMPANY LLC

CELGENE ALPINE INVESTMENT CO., LLC