SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Schedule 13D

Under the Securities Exchange Act of 1934

(Amendment No. 2)*

(Name of Issuer)

(Title of Class of Securities)

(CUSIP Number)

Bryan H. Lawrence

Yorktown Energy Partners VI, L.P.

410 Park Avenue

19th Floor

New York, New York 10022

(212) 515-2100

Copies to:

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

(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 204.13d-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 Rule 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).

This Amendment No. 2 amends the Schedule 13D with respect to the common units representing limited partner interests (“Common Units”) of Mid-Con Energy Partners, LP, a Delaware limited partnership (the “Company”), previously filed by Yorktown Energy Partners VI, L.P., a Delaware limited partnership (“Yorktown”), with the SEC on December 30, 2011, as amended by Amendment No. 1 filed with the SEC on October 24, 2012 (the “Schedule 13D”). Capitalized terms used herein without definition shall have the meanings given to such terms in the Schedule 13D.

Item 5. Interest in Securities of the Issuer.

Subparagraphs a and c of Item 5 of the Schedule 13D are amended and restated in their entirety by the following:

(a) As of March 11, 2013, Yorktown, Yorktown Company and Yorktown Associates beneficially owned 1,255,165 Common Units, representing 6.5% of the Company’s outstanding Common Units. All calculations made herein are made in accordance with Rule 13d-3(d) of the Securities Exchange Act of 1934, as amended, and based on 19,230,350 Common Units of the Company outstanding as of March 6, 2013, as set forth in the Company’s annual report on Form 10-K for the year ended December 31, 2012, filed with the SEC on March 6, 2013.

(c) On March 11, 2013, Yorktown distributed in-kind, on a pro rata basis and for no additional consideration, in accordance with its limited partnership agreement, an aggregate of 600,000 Common Units of the Company, to its limited and general partners (the “Distribution”). Upon the consummation of the Distribution by Yorktown, Yorktown Company distributed in-kind, on a pro rata basis and for no additional consideration, in accordance with its limited partnership agreement, all 127,094 Common Units of the Company received in the Distribution to its limited and general partners (the “Subsequent Distribution”). Upon the consummation of the Subsequent Distribution by Yorktown Company, Yorktown Associates distributed in-kind, on a pro rata basis and for no additional consideration, in accordance with its operating agreement, all 657 Common Units of the Company received in the Subsequent Distribution to its members.

SIGNATURES

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.

Date: March 12, 2013