SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE

13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a)

(Amendment No. 5)

Rex Energy Corporation

(Name of Issuer)

Common Stock

(Title of Class of Securities)

761565100

(CUSIP Number)

Lance T. Shaner

c/o Rex Energy Corporation

366 Walker Drive

State College, Pennsylvania 16801 (814) 278-7267

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

April 10, 2013, May 30, 2013, August 14, 2013, August 15, 2013

(Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box. ¨

Note:  Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See §240.13d-7 for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

SCHEDULE 13D

This Amendment No. 5 (this “Amendment”) amends and supplements the Statement on Schedule 13D, as previously amended (the “Schedule 13D”), relating to the shares of the common stock, par value $0.001 per share (the “Common Stock”) of Rex Energy Corporation, a Delaware corporation whose principal executive offices are located at 366 Walker Drive, State College, Pennsylvania 16801 (the “Issuer”), previously filed by Lance T. Shaner (the “Reporting Person”). This Amendment is being filed to update the Schedule 13D in light of recent events.

Unless otherwise indicated, all capitalized terms used herein shall have the meanings given to them in the Schedule 13D, and unless amended or supplemented hereby, all information previously filed remains in effect.

Item 1 is hereby amended and restated as follows:

This Schedule 13D relates to the Common Stock, par value $0.001 per share (the “Common Stock”) of Rex Energy Corporation, a Delaware corporation whose principal executive offices are located at 366 Walker Drive, State College, Pennsylvania 16801 (the “Issuer”).

Item 2 is hereby amended to add the following:

The business address of the Reporting Person is c/o Rex Energy Corporation, 366 Walker Drive, State College, Pennsylvania 16801.

Item 4 is hereby amended to add the following:

On April 10, 2013, the Shaner 2009 Spousal Remainder Trust (the “Spousal Trust”) transferred 5,736 shares of Common Stock to each of Mathias and Andrea Shaner, Justin and Monica Shaner, and Sarah S. Lykens, without payment or other consideration, representing an aggregate transfer of 17,208 shares of Common Stock.

On May 30, 2013, the Reporting Person transferred 14,561 shares of Common Stock to a third party without payment or consideration to the Reporting Person, as transferor.

On August 14, 2013, Shaner Family Partners Limited Partnership (“SFPLP”) sold 225,000 shares of Common Stock at a weighted average price of $21.27 per share pursuant to a Form 144 Notice of Proposed Sale of Securities (“Form 144”).

On August 14, 2013, Shaner Capital L.P. (“SCLP”) sold 126,734 shares of Common Stock at a weighted average price of $21.27 per share pursuant to a Form 144.

On August 15, 2013, the Spousal Trust sold 50,000 shares of Common Stock at a weighted average price of $20.01 per share pursuant to a Form 144.

On August 15, 2013, SCLP sold 98,266 shares of Common Stock at a weighted average price of $21.27 per share pursuant to a Form 144.

On August 15, 2013, the Reporting Person sold 2,000,000 shares of Common Stock at a weighted average price of $20.01 per share pursuant to a Form 144.

The purpose of the Reporting Person’s or other person’s acquisition or disposition, as applicable, of the shares of Common Stock disclosed above was for investment, estate planning and charitable purposes.

Item 5 is hereby amended and restated as follows:

(a) The Reporting Person may be deemed to be the beneficial owner of 3,829,898 shares of Common Stock, including:

(i) 2,964,777 shares of Common Stock directly owned by the Reporting Person;

(ii) 14,234 shares of restricted stock directly owned by the Reporting Person;

(iii) exercisable stock options directly owned by the Reporting Person, representing the right to acquire 22,743 shares of Common Stock;

(iv) 375,000 shares of Common Stock owned by SCLP—the Reporting Person is the sole member of Shaner Capital, LLC, a Delaware limited liability company, the general partner of SCLP;

(v) 296,678 shares of Common Stock owned by SFPLP—the Reporting Person is the sole member-manager of LT Shaner, LLC, a Delaware limited liability company, the general partner of SFPLP;

(vi) 39,229 shares of Common Stock owned by The Lance T. Shaner Irrevocable Grandchildren’s Trust II (the “Trust II”)—the Reporting Person is co-trustee of the Trust II;

(vii) 108,000 shares of Common Stock owned by the Shaner Family Foundation (the “Foundation”)—the Reporting Person is co-trustee of the Foundation; and

(viii) 9,246 shares of Common Stock owned by the Spousal Trust—the Reporting Person is co-trustee of the Spousal Trust.

The Reporting Person beneficially owns 7.1% of the issued and outstanding Common Stock.

b) The Reporting Person has the sole right to vote and dispose, or direct the disposition, of the 2,964,777 shares of Common Stock owned by the Reporting Person, the 14,234 shares of restricted stock owned by the Reporting Person, the exercisable stock options owned by the Reporting Person representing the right to acquire 22,743 shares of Common Stock, the 296,678 shares of Common Stock owned by SFPLP and the 375,000 shares of Common Stock owned by SCLP. The Reporting Person has the shared right to vote and dispose, or direct the vote and disposition, of:

(i) 39,229 shares of Common Stock owned by the Trust II;

(ii) 108,000 shares of Common Stock owned by the Foundation; and

(iii) 9,246 shares of Common Stock owned by the Spousal Trust.

The Reporting Person has the shared power to vote or direct the vote and dispose or direct the disposition of the shares of Common Stock owned by the Trust II with Ellen R. Shaner, as co-trustees of the Trust II. The Reporting Person has the shared power to vote or direct the vote and dispose or direct the disposition of the shares of Common Stock owned by the Foundation with Ellen R. Shaner, Sarah S. Lykens, Mathias Shaner and Justin Shaner, as co-trustees of the Foundation. The Reporting Person has the shared power to vote or direct the vote and dispose or direct the disposition of the shares of Common Stock owned by the Spousal Trust with Ellen R. Shaner and Kenneth P. Friedman, as co-trustees of the Spousal Trust. Kenneth P. Friedman, Sarah S. Lykens, Ellen R. Shaner, Justin Shaner and Mathias Shaner are collectively referred to as the “Trustees.”

The information with respect to the Trustees required by Item 2 is as follows:

The business address of each of the Trustees is c/o Shaner Hotel Group, 1965 Waddle Road, State College, Pennsylvania 16801.

Kenneth P. Friedman is a Partner at Hodgson Russ LLP, The Guaranty Building, 140 Pearl Street, Suite 100, Buffalo, New York 14202.

Sarah S. Lykens is the daughter of the Reporting Person. She is a manager member of Saharra Homes LLC, 1639 Sabal Palm Drive, Boca Raton, Florida 33432.

Ellen R. Shaner is the wife of the Reporting Person. Her principal occupation is that of a homemaker.

Justin Shaner is the son of the Reporting Person. He is the founder of JLS Creative Solutions, 255 Alhambra Circle, Suite 416, Coral Gables, Florida 33134.

Mathias Shaner is the son of the Reporting Person. He is the President and CEO of Shaner Investments L.P., One PPG Place, Suite 2370, Pittsburgh, Pennsylvania 15222.

To the best of the information and belief of the Reporting Person, during the past five years from the date of this Amendment, none of the Trustees has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors) or been party to a civil proceeding of a judicial or administrative body of competent jurisdiction as a result of which proceeding any of them was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

Each of the Trustees is a citizen of the United States of America.

(c) Other than as set forth herein, during the 60-day period ended August 26, 2013, the Reporting Person did not purchase or sell any shares of Common Stock.

(d) Other than the Reporting Person, the following persons may have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, the shares of Common Stock reported herein:

(e) Not applicable.

The Reporting Person disclaims beneficial ownership of the shares held by the Trust II, SFPLP, SCLP, the Spousal Trust and the Foundation, and this schedule shall not be deemed an admission that the Reporting Person is the beneficial owner of such shares.

Item 6 is hereby amended to add the following:

The Reporting Person is a party to a Commercial Pledge Agreement by and between the Reporting Person and Susquehanna Bank, as successor in interest to Graystone Bank (“Susquehanna”), pursuant to which the Reporting Person has pledged 272,000 shares of Common Stock to secure a business line of credit extended by Susquehanna to the Reporting Person.

The Reporting Person is a party to a Commercial Pledge Agreement by and between the Reporting Person and JP Morgan Chase Bank, N.A. (“JP Morgan”), pursuant to which the Reporting Person has pledged 2,134,777 shares of Common Stock to secure a business line of credit extended by JP Morgan to the Reporting Person.

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.