UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d)

of The Securities Exchange Act of 1934

Date of Report (Date of Earliest Event Reported): June 30, 2016

Zafgen, Inc.

(Exact name of registrant as specified in its charter)

Registrant’s telephone number, including area code (617) 622-4003

Not Applicable

(Former name or former address, if changed since last report)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

Zafgen, Inc. (the “Company” or “we”) held its Annual Meeting of Stockholders (the “Annual Meeting”) on June 30, 2016. As of May 2, 2016, the record date for the Annual Meeting, there were 27,272,261 outstanding shares of the Company’s common stock. The Company’s stockholders voted on the following matters, which are described in detail in the Company’s Definitive Proxy Statement filed with the U.S. Securities and Exchange Commission (“SEC”) on May 4, 2016: (i) to elect Peter Barrett, Ph.D., Frances K. Heller and Bruce Booth, Ph.D. as Class II directors of the Company to each serve for a three-year term expiring at the Company’s annual meeting of stockholders in 2019 and until their successors have been duly elected and qualified (“Proposal 1”), and (ii) to ratify the appointment of PricewaterhouseCoopers LLP as the Company’s independent registered public accounting firm for the fiscal year ending December 31, 2016 (“Proposal 2”).

The Company’s stockholders approved the Class II director nominees recommended for election in Proposal 1 at the Annual Meeting. The Company’s stockholders voted for Class II directors as follows:

The Company’s stockholders approved Proposal 2. The votes cast at the Annual Meeting were as follows:

No other matters were submitted to or voted on by the Company’s stockholders at the Annual Meeting.

On June 30, 2016, we entered into severance and change in control agreements with our executive officers, including Dr. Thomas E. Hughes, our Chief Executive Officer, Patrick Loustau, our President, Alicia Secor, our Chief Commercial Officer, Patricia L. Allen, our Chief Financial Officer, and Dr. Dennis Kim, our Chief Medical Officer (each, an “Executive” and collectively, the “Executives”). The terms of these new severance and change in control agreements supersede any terms of prior employment agreements or offer letters of these Executives providing for payments or benefits upon severance or a change of control. The new severance and change in control agreements entitle each Executive to certain payments and benefits in the event that such Executive’s employment is terminated by us without “cause” (as defined below), such Executive terminates his or her employment with “good reason” (as defined below), or such Executive’s employment is terminated without “cause” or the Executive terminates his or her employment for “good reason” within 12 months of a “change of control” (as defined below).

Pursuant to the new severance and change in control agreements, in the event that Dr. Hughes terminates his employment with “good reason” or is terminated without “cause,” Dr. Hughes is eligible to receive 12 months of base salary continuation and 12 months of COBRA continuation medical benefits subsidized by us, provided that he executes and does not revoke a separation agreement and release of us and our affiliates. In the event that Dr. Hughes’ employment is terminated without “cause” or Dr. Hughes terminates his employment for “good reason” within 12 months of a “change of control,” Dr. Hughes is eligible to receive 18 months of base salary continuation, 18 months of COBRA continuation medical benefits subsidized by us, and all options and other stock-based awards held by him shall immediately accelerate and become fully exercisable or non-forfeitable as of the date of termination, provided that he executes and does not revoke a separation agreement and release of us and our affiliates.

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Pursuant to his or her new severance and change in control agreement, in the event that Mr. Loustau, Ms. Secor, Ms. Allen, or Dr. Kim terminates his or her employment with “good reason” or is terminated without “cause,” such Executive is eligible to receive 9 months of base salary continuation and 9 months of COBRA continuation medical benefits subsidized by us, provided that he or she executes and does not revoke a separation agreement and release of us and our affiliates. In the event that Mr. Loustau’s, Ms. Secor’s, Ms. Allen’s, or Dr. Kim’s employment is terminated without “cause” or such Executive terminates his or her employment for “good reason” within 12 months of a “change of control”, such Executive is eligible to receive 12 months of base salary continuation and 12 months of COBRA continuation medical benefits subsidized by us, and all options and other stock-based awards held by such Executive shall immediately accelerate and become fully exercisable or non-forfeitable as of the date of termination, provided that he or she executes and does not revoke a separation agreement and release of us and our affiliates.

For purposes of the new severance and change in control agreements, “cause” means:

For purposes of the new severance and change in control agreements, “good reason” means:

For purposes of the new severance and change in control agreements, a “change in control” shall be deemed to have occurred upon the occurrence of any one of the following events:

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

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