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): March 12, 2015

SUNESIS PHARMACEUTICALS, INC.

(Exact name of registrant as specified in its charter)

Registrant’s telephone number, including area code: (650) 266-3500

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 August 11, 2011, we entered into a Controlled Equity Offering^SM sales agreement, or the Sales Agreement, with Cantor Fitzgerald & Co., or Cantor, as agent and/or principal, pursuant to which we may issue and sell shares of our common stock par value $0.0001 per share. On April 10, 2013, we amended the Sales Agreement, or the First Sales Agreement Amendment, to primarily provide for an increase in the aggregate gross sales price under the Sales Agreement. On March 12, 2015, we entered into a second amendment to the Sales Agreement, or the Second Sales Agreement Amendment, to primarily provide for an increase in the aggregate gross sales price under the Sales Agreement by an additional $30.0 million.

Under the Sales Agreement, as amended, Cantor may sell our common stock by methods deemed to be an “at-the-market” offering as defined in Rule 415 promulgated under the Securities Act of 1933, as amended, or the Securities Act, including sales made directly on The NASDAQ Stock Market on any other existing trading market for the Common Stock or to or through a market maker. In addition, under the Sales Agreement, as amended, Cantor may sell our common stock by any other method permitted by law, including in privately negotiated transactions. We may instruct Cantor not to sell our common stock if the sales cannot be effected at or above the price designated by us from time to time.

We will pay Cantor a commission rate of up to 3.0% of the gross sales price per share of any common stock sold through Cantor as agent under the sales agreement. We have also provided Cantor with customary indemnification and contribution rights.

Under the terms of the Sales Agreement, as amended, we may also sell shares of our common stock to Cantor, as principal for its own account, at a price negotiated at the time of sale. If we sell shares to Cantor in this manner, we will enter into a separate agreement setting forth the terms of any such transactions.

The foregoing description of the Sales Agreement is not complete and is qualified in its entirety by reference to the full text of such agreement, a copy of which was filed as Exhibit 10.1 to our Current Report on Form 8-K filed with the Securities and Exchange Commission on August 11, 2011 and is incorporated by reference herein. The foregoing description of the Second Sales Agreement Amendment is qualified in its entirety by reference to the full text of such agreement, which is filed herewith as Exhibit 10.1 to this Current Report on Form 8-K and is incorporated by reference herein. This Current Report on Form 8-K also incorporates by reference the Second Sales Agreement Amendment into our shelf registration statement on Form S-3 (File No. 333-195779) previously filed with the Securities and Exchange Commission.

The opinion of our counsel regarding the validity of the Common Stock that will be issued pursuant to the Sales Agreement, as amended, is also filed herewith as Exhibit 5.1.

(d) Exhibits

SIGNATURE

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