UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 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):

December 15, 2015

Pfenex Inc.

(Exact name of registrant as specified in its charter)

10790 Roselle Street

San Diego, CA 92121

(Address of principal executive offices, including zip code)

(858) 352-4400

(Registrant’s telephone number, including area code)

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 (see General Instruction A.2. below):

On December 15, 2015, Pfenex Inc. (the “Company”) entered into an underwriting agreement (the “Underwriting Agreement”) with The Dow Chemical Company (the “Selling Stockholder”), and Morgan Stanley & Co. LLC (the “Underwriter”), pursuant to which the Selling Stockholder agreed to sell 600,000 shares of our common stock, par value $0.001 per share (the “Common Stock”) to the Underwriter (the “Offering”). The Offering is expected to close on December 21, 2015, subject to the satisfaction of the closing conditions set forth in the Underwriting Agreement.

The Company is not selling any shares in the Offering and will not receive any proceeds from the sale of the Common Stock by the Selling Stockholder in the Offering.

The Offering is being made pursuant to the Company’s effective registration statement on Form S-3 (Registration Statement No. 333-206625) previously filed with and declared effective by the Securities and Exchange Commission (the “SEC”) and a prospectus supplement thereunder.

The Underwriting Agreement contains customary representations, warranties and agreements by the Company, customary conditions to closing, indemnification obligations of the parties, including for liabilities under the Securities Act of 1933, as amended (the “Securities Act”), other obligations of the parties and termination provisions. The representations, warranties and covenants contained in the Underwriting Agreement were made only for purposes of such agreement and as of specific dates, were solely for the benefit of the parties to such agreement, and may be subject to limitations agreed upon by the contracting parties. A copy of the Underwriting Agreement is attached as Exhibit 1.1 to this report and is incorporated by reference herein. The foregoing description of the terms of the Underwriting Agreement does not purport to be complete and is qualified in its entirety by reference to such exhibit.

The legal opinion of Wilson Sonsini Goodrich & Rosati, Professional Corporation relating to the legality of the Common Stock being offered is filed as Exhibit 5.1 to this Current Report on Form 8-K.

On December 16, 2015, the Company issued a press release related to the Offering. The press release is attached hereto as Exhibit 99.1 and is incorporated herein by reference.

(d) Exhibits

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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