SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

(Rule 13d-101)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO § 240.13d-1(a) AND AMENDMENTS THERETO FILED

PURSUANT TO § 240.13d-2(a)

Under the Securities Exchange Act of 1934

(Amendment No. 5)*

Chipotle Mexican Grill, Inc.

(Name of Issuer)

Common Stock, par value $0.01 per share

(Title of Class of Securities)

169656105

(CUSIP Number)

Steve Milankov, Esq.

Pershing Square Capital Management, L.P.

888 Seventh Avenue, 42nd Floor

New York, New York 10019

(212) 813-3700

With a copy to:

Richard M. Brand, Esq.

Cadwalader, Wickersham & Taft LLP

One World Financial Center

New York, NY 10281

(212) 504-6000

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

August 28, 2018

(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 which 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).

This amendment No. 5 (the “Amendment No. 5”) to Schedule 13D relates to the Schedule 13D filed on September 6, 2016 (the “Original Schedule 13D”, as amended and supplemented through the date of this Amendment No. 5, the “Schedule 13D”) by (i) Pershing Square Capital Management, L.P., a Delaware limited partnership (“Pershing Square”), (ii) PS Management GP, LLC, a Delaware limited liability company (“PS Management”) and (iii) William A. Ackman, a citizen of the United States (together with Pershing Square and PS Management, the “Reporting Persons”) relating to the common stock, par value $0.01 per share (the “Common Stock”), of Chipotle Mexican Grill, Inc., a Delaware corporation (the “Issuer”).

Capitalized terms used but not defined in this Amendment No. 5 shall have the meanings set forth in the Schedule 13D.

Except as specifically amended by this Amendment No. 5, the Schedule 13D is unchanged.

The second and third paragraphs of Item 1 of the Original Schedule 13D is hereby amended and restated in full to read as follows:

“The Reporting Persons beneficially own 2,059,106 shares of Common Stock (the “Subject Shares”).

The Subject Shares represent approximately 7.4% of the outstanding shares of Common Stock based on 27,804,105 shares of Common Stock outstanding as of July 23, 2018 as reported in the Issuer’s Quarterly Report on Form 10-Q filed on July 27, 2018 for the calendar quarter ended June 30, 2018.”

Item 4 of the Original Schedule 13D is hereby amended and supplemented by adding the following information:

“On August 28, 2018, the Reporting Persons on behalf of the Pershing Square Funds sold Common Stock for portfolio management purposes in open market transactions and in a block transaction with a broker.”

Item 5 of the Original Schedule 13D is hereby amended and supplemented by adding the following information:

“(a), (b) Information about the number and percentage of shares of Common Stock beneficially owned by the Reporting Persons is set forth in Item 1, and that information is incorporated by reference herein.

(c) Exhibit 99.8 filed herewith, which is incorporated by reference into this Item 5(c) as if restated in full, describes all of the transactions in the Common Stock or derivatives relating to Common Stock that were effected in the past 60 days by the Reporting Persons for the benefit of the Pershing Square Funds. Except as set forth in Exhibit 99.8, no reportable transactions were effected by any Reporting Person within the last 60 days.”

Item 7 of the Original Schedule 13D is hereby amended and supplemented by adding a reference to the following exhibit:

SIGNATURE

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

Dated: August 30, 2018

INDEX TO EXHIBITS