UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

FORM 10-K/A

Amendment No. 3

(Mark One)

For the fiscal year ended December 31, 2013

OR

Commission File No. 0-16203

PAR PETROLEUM CORPORATION

(Exact name of registrant as specified in its charter)

Registrant’s telephone number, including area code: (281) 899-4800

Securities registered under Section 12(b) of the Act: None

Securities registered under to Section 12(g) of the Act: Common stock, par value $0.01 per share

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.    Yes  ¨    No  x

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.    Yes  ¨    No  x

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Website, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes x No ¨

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or smaller reporting company. See definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act).    Yes  ¨    No  x

Indicate by check mark whether the registrant has filed all document and reports required to be filed by Sections 12, 13 or 15 (d) of the Securities Exchange Act of 1934 subsequent to the distribution of securities under a plan confirmed by a court.    Yes  x    No  ¨

The aggregate market value of voting common equity held by non-affiliates of the registrant was approximately $55,000,000 based on the closing price of the common stock on the OTCQB Marketplace of $16.30 per share as of June 28, 2013. As of March 26, 2014, 30,159,039 shares of registrant’s Common Stock, $0.01 par value, were issued and outstanding.

Documents Incorporated By Reference

None.

EXPLANATORY NOTE

Par Petroleum Corporation (the “Company,” “we,” “our,” and “us”) is filing this Amendment No. 3 to Annual Report on Form 10-K/A (this “Amended Form 10-K”) to amend its Annual Report on Form 10-K for the fiscal year ended December 31, 2013, as originally filed with the U.S. Securities and Exchange Commission (the “SEC”) on March 31, 2014, and amended by Amendment No. 1on Form 10-K/A filed with the SEC on April 29, 2014 and Amendment No. 2 on Form 10-K/A filed with the SEC on May 30, 2014 (collectively, the “Original Form 10-K”), solely in response to comments received from the staff of the SEC. In response to the comments, the Company amended the Original Form 10-K to (i) expand its disclosure regarding the compensation paid to a consulting firm for the services of two named executive officers during the years ended December 31, 2012 and 2013, (ii) explain the differences in the salaries received during 2013 by the named executive officers and (iii) file as exhibits its employment offer letters and award notices of restricted stock with certain named executive officers and its agreement with Conway MacKenzie Management Services, LLC. In addition, the Company has amended the summary of William Monteleone’s employment arrangement to correct an error in the disclosure regarding his annual salary.

In accordance with Rule 12b-15 under the Securities and Exchange Act of 1934, as amended, Item 11 of Part III of the Original Form 10-K, and Item 15 of Part IV of the Original Form 10-K are hereby amended and restated in their entirety. This Amended Form 10-K does not amend or otherwise update any other information in the Original Form 10-K. Accordingly, this Amended Form 10-K should be read in conjunction with the Original Form 10-K and with our subsequent filings with the SEC. All capitalized terms used but not defined herein shall have the meanings ascribed to them in the Original Form 10-K.

PART III

In connection with our emergence from bankruptcy on August 31, 2012, John T. Young, Jr. was engaged as our Chief Executive Officer until June 2013 and R. Seth Bullock was engaged as our Chief Financial Officer until December 2013. Messrs. Young and Bullock were our only executive officers until the assembly of our management team during 2013. Messrs. Young and Bullock were also employees of Conway MacKenzie Management Services, LLC (“Conway MacKenzie”), with whom we had a management and financial advisory services agreement dated November 8, 2011. During 2013, we hired Messrs. Monteleone, Coxon, Micklas and Tarzwell to serve as our Chief Executive Officer, Chief Operating Officer, Chief Financial Officer and Chief Legal Officer, respectively.

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The current members of the Compensation Committee of the Board did not serve on the Compensation Committee prior to our emergence from bankruptcy on the Emergence Date. Pursuant to the charter of the Compensation Committee adopted subsequent to our emergence from bankruptcy, it is the duty of the Compensation Committee to, among other things, develop and approve our compensation philosophy and objectives, review and determine the amount and mix of total compensation of our executive officers, develop, administer and review our employment agreements, incentive plans and other compensation programs, and oversee the risk assessment of our compensation arrangements.

We have recently completed the assembly of our management team and are in the process of developing our compensation philosophies and compensation objectives and policies.

Summary Compensation

The following table sets forth information regarding compensation earned during the last two fiscal years by our Chief Executive Officer, our Chief Operating Officer, our Senior Vice President and Chief Legal Officer and our former Chief Executive Officer (the “Named Executive Officers”).

SUMMARY COMPENSATION TABLE

Narrative Disclosure to Summary Compensation Table

See “– Employment Agreements” below for a discussion of the employment arrangements with our Named Executive Officers. See the footnotes to the Summary Compensation Table for narrative disclosure with respect to that table.

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Outstanding Equity Awards at Fiscal Year-End

The following table sets forth certain information with respect to the market value of all unvested share awards held by each Named Executive Officer as of December 31, 2013.

Employment Agreements

On September 25, 2013, the Company entered into an “at will” employment arrangement with William Monteleone, the Company’s Chief Executive Officer. Mr. Monteleone is entitled to receive an annual base salary of $200,000 paid no less frequently than on a semi-monthly basis in accordance with Company payroll practices. Mr. Monteleone’s compensation will be reviewed annually. Mr. Monteleone is also eligible for an annual performance bonus as may be awarded in the sole discretion of the Board.

On September 25, 2013, Mr. Monteleone was granted $250,000 in restricted Company common stock pursuant to the 2012 Long Term Incentive Plan (the “Plan”). In addition, Mr. Monteleone was granted $250,000 in restricted Company common stock under the Plan on December 31, 2013. In each case, the actual number of shares granted was determined based on the average volume weighted average price of the Company’s common stock for the 60 days immediately preceding the date of grant. Subject to the terms thereof, these restricted stock grants will vest ratably over a 5-year period on each anniversary of the date of grant with 100% accelerated vesting for certain events such as a change in control of the Company.

Mr. Monteleone is also eligible to participate in any benefit plans that may be offered from time to time by the Company to its employees generally and in the Company’s 401(k) plan, in each case subject to his satisfaction of the applicable eligibility provisions. Mr. Monteleone is also entitled to airfare between Chicago and Houston and $2,500/month of living expenses.

On December 31, 2012, the Company entered into an “at will” employment arrangement with Peter Coxon, the Company’s Chief Operating Officer. Mr. Coxon is entitled to receive an annual base salary of $250,000 paid no less frequently than on a semi-monthly basis in accordance with the Company’s payroll practices. Mr. Coxon’s compensation will be reviewed annually. On March 14^, 2014, Mr. Coxon’s base salary was increased to $350,000. In connection with his salary increase, Mr. Coxon was paid $40,143 as additional salary for 2013.

On December 31, 2012, Mr. Coxon was granted $1,500,000 in restricted Company common stock under the Plan. The actual number of shares granted was determined based on the average volume weighted price of the Company’s common stock for the 60 days immediately preceding the date of grant. The restricted stock grant vests ratably over a 5-year period on each anniversary of the grant with 100% accelerated vesting for certain events such as a change in control of the Company.

For the year ended December 31, 2013, Mr. Coxon was also eligible to participate in a 20% profit sharing program focusing on our commodity marketing and logistics business with the allocation of his bonus determined upon his performance and contributions to the profitability of that segment. In March 2014, he received a bonus payment of $839,983 related to 2013 performance.

Mr. Coxon is also eligible to participate in any benefit plans that may be offered from time to time by the Company to its employees generally and in the Company’s 401(k) plan, in each case subject to his satisfaction of the applicable eligibility provisions.

On May 22, 2013, the Company entered into an “at will” employment arrangement with Mr. Tarzwell, pursuant to which Mr. Tarzwell is entitled to receive an annual base salary of $250,000 paid in accordance with Company payroll practices. Mr. Tarzwell is also eligible for an annual performance bonus, based on the discretion of the Compensation Committee of the Board.

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On May 22, 2013, Mr. Tarzwell was granted $175,000 in restricted Company common stock under the Plan. In addition, Mr. Tarzwell will be granted $175,000 in restricted Company common stock under the Plan upon completing one year of employment. In each case, the actual number of shares granted will be determined based on the average volume weighted average price of the Company’s common stock for the 60 days immediately preceding the date of grant. Subject to the terms thereof, these restricted stock grants will vest on the 24-month anniversary of the commencement of Mr. Tarzwell’s employment with 100% accelerated vesting for certain events such as a change in control of the Company.

Mr. Tarzwell is also eligible to participate in any benefit plans that may be offered from time to time by the Company to its employees generally and in the Company’s 401(k) plan, in each case subject to his satisfaction of the applicable eligibility provisions.

Potential Payments upon Termination or Change in Control

The shares of restricted stock granted to Messrs. Monteleone, Coxon and Tarzwell under the Plan will automatically vest in their entirety upon certain events such as a change of control or a termination of their employment due to death, disability or without cause.

The following tables further describe the potential payments upon termination or a change in control for Messrs. Monteleone, Coxon and Tarzwell.

William Monteleone

Chief Executive Officer

Peter Coxon

Chief Operation Officer

Brice Tarzwell

Chief Legal Officer and Senior Vice President

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Director Compensation

The following table sets forth a summary of the compensation that we paid to our non-employee directors in 2013:

In December 2012, we approved a compensation plan for our non-employee directors. Our non-employee directors receive an annual retainer of $50,000, paid quarterly in cash or shares of our common stock at the election of the director. In addition, the Chairman of the Audit Committee receives an additional annual retainer of $15,000 and the members of the Audit Committee (other than the Chairman) receive an annual retainer of $5,000, such retainers paid quarterly in cash or shares of our common stock at the election of the director. There are no fees for the members of any other committee or for attendance at meetings. Our non-employee directors are also entitled to receive an annual grant of restricted stock at the end of each calendar year with a target value of $75,000, with the number of shares determined by the 60-day volume weighted average share price as of the day prior to December 31 of that calendar year. Mr. Mercer waived his right to receive any of the compensation described in this paragraph in 2013. Mr. Keener and Mr. Cooper both received awards of 2,289 shares of common stock for their service in 2013. Messrs. Monteleone and Lurie elected to receive their annual retainer in shares of common stock, rather than cash, and as such, an additional 2,756 shares and 3,418 shares of common stock were issued to each of them during 2013.

Narrative Disclosure of Compensation Policies and Practices as Related to Risk Management

In accordance with the requirements of Regulation S-K, Item 402(s), to the extent that risks may arise from our compensation policies and practices that are reasonably likely to have a material adverse effect on us, we are required to discuss those policies and practices for compensating our employees (including employees that are not named executive officers) as they relate to our risk management practices and the possibility of incentivizing risk-taking. We have determined that the compensation policies and practices established with respect to our employees are not reasonably likely to have a material adverse effect on us and, therefore, no such disclosure is necessary.

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PART IV

(a)(1) Financial Statements.

The following financial statements were filed as part of Amendment No. 2 to the Company’s Annual Report on Form 10-K/A filed with the SEC on May 30, 2014.

(2) Financial Statement Schedules. None.

(3) Exhibits.

INDEX TO EXHIBITS

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8

9

10

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SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange of Act of 1934, the registrant has caused this Form 10-K/A to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of Houston and State of Texas on the 2^nd day of July, 2014.