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): July 30, 2013

CONATUS PHARMACEUTICALS INC.

(Exact Name of Registrant as Specified in its Charter)

Registrant’s telephone number, including area code: (858) 558-8130

(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 July 30, 2013, Conatus Pharmaceuticals Inc. (the “Company”) issued 91,948 shares of its common stock (the “Conversion Shares”) to certain of its stockholders in connection with the completion of the initial public offering of shares of its common stock (the “IPO”). The Conversion Shares were issued as a result of the automatic conversion of $1.0 million in aggregate principal amount of convertible promissory notes issued by the Company in May 2013, including accrued interest thereon, at a price per share of $11.00, the price at which shares of the Company’s common stock were sold to the public in the IPO (the “IPO Price”).

In addition, on July 30, 2013, the Company issued 280,675 shares (the “Exercise Shares”) of its common stock to certain of its stockholders in connection with the net exercise of warrants issued in 2010, based on a price per share equal to the IPO Price.

The sales and issuances by the Company of the Conversion Shares and Exercise Shares were not registered under the Securities Act of 1933, as amended (the “Securities Act”), or any state securities laws. The Company has relied on the exemption from the registration requirements of the Securities Act under Section 4(a)(2) thereof and/or Rule 506 of Regulation D promulgated under the Securities Act.

On July 30, 2013, in connection with closing of the IPO, the Company filed an amended and restated certificate of incorporation (the “Charter”) with the Secretary of State of the State of Delaware. The Company’s board of directors and stockholders previously approved the Charter to be filed in connection with the closing of the IPO.

The Charter amends and restates the Company’s certificate of incorporation in its entirety to, among other things: (i) increase the authorized number of shares of common stock to 200,000,000 shares; (ii) eliminate all references to the previously existing series of preferred stock; (iii) authorize 10,000,000 shares of undesignated preferred stock that may be issued from time to time by the Company’s board of directors in one or more series; (iv) establish a classified board of directors, divided into three classes, each of whose members will serve for staggered three-year terms; (v) provide that directors may be removed from office only for cause and only upon the affirmative vote of the holders of at least two-thirds of the holders of the Company’s capital stock entitled to vote; and (vi) eliminate the ability of the Company’s stockholders to take action by written consent in lieu of a meeting and call special meetings of stockholders.

The foregoing description of the amendments made by the Charter is qualified by reference to the Charter, a copy of which is attached hereto as Exhibit 3.1 and is incorporated herein by reference.

On July 30, 2013, in connection with the closing of the IPO, amended and restated bylaws of the Company (the “Bylaws”), previously approved by the Company’s board of directors and stockholders to become effective in connection with closing of the IPO, became effective. The Bylaws amend and restate the Company’s bylaws in their entirety to, among other things: (i) eliminate the ability of the Company’s stockholders to take action by written consent in lieu of a meeting and call special meetings of stockholders; (ii) establish procedures relating to the presentation of stockholder proposals at stockholder meetings; (iii) establish procedures relating to the nomination of directors; and (iv) conform to the amended provisions of the Charter.

The foregoing description of the amendments made in the Bylaws is qualified by reference to the Bylaws, a copy of which is attached hereto as Exhibit 3.2 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.

EXHIBIT INDEX