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): January 7, 2016

IGNYTA, INC.

(Exact Name of Registrant as Specified in its Charter)

11111 Flintkote Avenue

San Diego, California 92121

(Address of principal executive offices, including zip code)

Registrant’s telephone number, including area code: (858) 255-5959

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:

1. Base Salaries for Named Executive Officers. On January 7, 2016, the Compensation Committee of the Board of Directors (the “Committee”) of Ignyta, Inc. (the “Company”) established the base salaries to be paid to the Company’s named executive officers listed below (the “Named Executive Officers”), effective retroactively to January 1, 2016. In determining individual salaries, the Committee considered various factors, including an individual’s qualifications and relevant experience, the scope of the executive’s job responsibilities, individual contributions and performance, and the compensation levels of executives at similar companies. The following 2016 base salaries were established:

2. Bonuses Payable to Named Executive Officers. Also on January 7, 2016, the Committee approved cash bonuses to be paid to the Named Executive Officers. The bonuses related to such officers’ performance and the Company’s performance during 2015. The bonuses to be paid to the Named Executive Officers are as follows:

3. RSU Grants. Also on January 7, 2016, the Committee granted restricted stock units (“RSUs”) to the Named Executive Officers under the Company’s 2014 Incentive Award Plan (the “Plan”). The RSUs related to such officers’ performance and the Company’s performance during 2015. The number of RSUs received by each Named Executive Officer is as follows:

All of such RSUs will initially be unvested and will vest as follows, subject in each case to the Named Executive Officer’s continued employment with the Company: all of the RSUs will vest on January 7, 2021, provided that all of such RSUs will immediately vest upon the consummation of a Change in Control (as such term is defined in the Plan).

4. Amendments to Severance Plan. Also on January 7, 2016, the Committee amended the Company’s Severance and Change in Control Severance Plan (the “Severance Plan”), as follows:

The foregoing description of the amendments to the Severance Plan is subject to, and qualified in its entirety by reference to, the Amended and Restated Severance Plan, which the Company intends to file with its Quarterly Report on Form 10-Q for the quarter ended March 31, 2016. A description of the terms and provisions of the Severance Plan prior to such amendments is set forth in the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission on December 19, 2013, which description is incorporated herein by reference.

5. Annual Cash Bonus Targets. Also on January 7, 2016, the Committee set the target percentages for determining annual bonuses for the Named Executive Officers for 2016, expressed as a percentage of the applicable executive officer’s annual base salary, as follows:

The target represents a target cash bonus amount, eligibility for all or a portion of which will be subject to (i) the applicable Named Executive Officer’s achievement of performance objectives, determined annually by the Committee, and (ii) the discretion of the Committee to approve bonus amounts that are higher or lower than the stated target.

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.