SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 5)*

CommonWealth REIT

(Name of Issuer)

Common Shares of Beneficial Interest, par value $0.01 per share

(Title of Class of Securities)

203233101

(CUSIP Number)

Keith Meister

Corvex Management LP

712 Fifth Avenue, 23rd Floor

New York, New York 10019

(212) 474-6700

Richard O’Toole

Related Fund Management, LLC

60 Columbus Circle

New York, New York 10023

(212) 421-5333

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

March 13, 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 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. 5 to the Schedule 13D (this “Amendment No. 5”) relates to the common shares of beneficial interest, par value $0.01 per share (the “Shares”), of CommonWealth REIT, a Maryland real investment trust (the “Issuer” or “CommonWealth”) and amends the Schedule 13D filed on February 26, 2013, as amended by Amendment No. 1 thereto, filed with the SEC on February 27, 2013, Amendment No. 2 thereto, filed with the SEC on March 4, 2013, Amendment No. 3 thereto, filed with the SEC on March 4, 2013, and Amendment No. 4 thereto, filed with the SEC on March 11, 2013 (the “Original Schedule 13D” and, together with this Amendment No. 5, the “Schedule 13D”). Capitalized terms used and not defined in this Amendment No. 5 have the meanings set forth in the Original Schedule 13D.

This Amendment No. 5 is being filed by (i) Corvex Management LP, a Delaware limited partnership (“Corvex”), and Keith Meister and (ii) Related Fund Management, LLC, a Delaware limited liability company (“Related”), Related Real Estate Recovery Fund GP-A, LLC, a Delaware limited liability company, Related Real Estate Recovery Fund GP, L.P., a Delaware limited partnership, Related Real Estate Recovery Fund, L.P., a Delaware limited partnership, and RRERF Acquisition, LLC, a Delaware limited liability company.

This Amendment No. 5 is being filed to amend Item 3, Item 4, Item 5 and Item 7 of the Schedule 13D as follows:

Item 3 of the Schedule 13D is amended and restated to read as follows:

The Reporting Persons may be deemed to be the beneficial owner of, in the aggregate, 10,165,500 Shares. The aggregate purchase price of such Shares was approximately $183.36 million (including commissions and premiums). The Shares were acquired with working capital of the Corvex Funds and Related Recovery Fund.

The Reporting Persons may effect purchases of Shares through margin accounts maintained for them with brokers, which extend margin credit as and when required to open or carry positions in their margin accounts, subject to applicable federal margin regulations, stock exchange rules and such firms’ credit policies. Positions in Shares may be held in margin accounts and may be pledged as collateral security for the repayment of debit balances in such accounts. Such margin accounts may from time to time have debit balances. In addition, since other securities may be held in such margin accounts, it may not be possible to determine the amounts, if any, of margin used to purchase shares of Shares.

The information set forth under Item 6 is incorporated in this Item 3 in its entirety.

Item 4 of the Schedule 13D is amended by adding the following:

On March 12, 2013, Corvex and Related sent a letter to the independent trustees of the Issuer reiterating their request to meet with the Issuer. Corvex and Related further requested that the independent trustees form a special committee and cease any plans to enter into any extraordinary transactions that could further erode shareholder value, including any related-party transactions.

On March 13, 2013, Corvex and Related issued a press release regarding their filing of a preliminary written consent solicitation statement with the SEC for shareholders to act by written consent to effect the removal of the entire board of trustees of the Issuer. The press release is attached as Exhibit 13 and incorporated by reference in this Item 4 in its entirety.

Paragraphs (a)-(c) of Item 5 of the Schedule 13D are amended and restated to read as follows:

(a)-(b) Each of the Corvex Persons may be deemed to be the beneficial owner of 10,165,500 Shares (representing approximately 8.6% of the Issuer’s outstanding Shares), which include: (i) 5,082,750 Shares held on behalf of the Corvex Funds (the “Corvex Shares”) and (ii) 5,082,750 Shares held on behalf of RRERF (the “Related Shares”). By virtue of his position as a control person of the general partner of Corvex, Mr. Meister and Corvex may be deemed to share voting power and dispositive power with respect to the Corvex Shares. In addition, by virtue of the Agreement, the Corvex Persons may be deemed to share with the Related Persons voting power and dispositive power with respect to the Related Shares. Each of the Corvex Persons disclaims beneficial ownership with respect to the Related Shares.

Each of the Related Persons may be deemed to be the beneficial owner of 10,165,500 Shares (representing approximately 8.6% of the Issuer’s outstanding Shares), which include: (i) the Related Shares and (ii) the Corvex Shares. By virtue of their relationship, as described in Item 2, the Related Persons may be deemed to share voting power and dispositive power with respect to the Related Shares. In addition, by virtue of the Agreement, the Related Persons may be deemed to share with the Corvex Persons voting power and dispositive power with respect to the Corvex Shares. Each of the Related Persons disclaims beneficial ownership with respect to the Corvex Shares.

The filing of this Schedule 13D shall not be construed as an admission that any of the Reporting Persons is the beneficial owner of any securities covered by the Schedule 13D.

(c) Except as set forth on Exhibit 5 to this Schedule 13D, there have been no transactions with respect to the Shares during the sixty days prior to the date of filing of this Schedule 13D by any of the Reporting Persons or, to their knowledge, any other person or entity referred to in Item 2 of this Schedule 13D.

Item 7 of the Schedule 13D is amended by adding thereto the following:

SIGNATURES

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

Exhibit 5

TRANSACTIONS

The following table sets forth all transactions effected in the last sixty days by or on behalf of the Reporting Persons in respect of the Shares, inclusive of any transactions effected through 4:00 p.m., New York City time, on March 12, 2013. All such transactions were purchases of Shares effected by Corvex in the open market and the table includes commissions paid in per share prices. Pursuant to the Agreement dated January 29, 2013 by and between Corvex and Related Recovery Fund, 50% of all Shares purchased by Corvex were allocated to a trading account established by Related Recovery Fund, and Related Recovery Fund promptly reimbursed Corvex at cost for the purchase price of such Shares.

Exhibit 13

CORVEX AND RELATED FILE PRELIMINARY CONSENT SOLICITATION STATEMENT

TO REMOVE ALL TRUSTEES OF COMMONWEALTH REIT (CWH)

Engage Deutsche Bank Securities Inc.

NEW YORK, March 13, 2013—Corvex Management LP (“Corvex”) and Related Fund Management, LLC (“Related”) announced today that they have filed a preliminary consent solicitation statement with the U.S. Securities and Exchange Commission for shareholders to act by written consent to effect the removal of the entire board of trustees of CommonWealth REIT (“CWH” or the “Company”). CWH’s charter expressly permits holders of two-thirds of the outstanding shares to remove trustees without cause by written consent.

Once shareholders have removed the current board of trustees, CWH’s charter requires that the officers of the Company immediately call a special meeting of shareholders to elect successor trustees. Corvex and Related believe that their proposal to remove the entire board of trustees as a first step, if supported by shareholders, will send a clear and unequivocal message to Barry Portnoy and his son, Adam, that the time has come for them to be held accountable to the true owners of CWH. This process also presents a clean path for all shareholders to fairly participate in the process of electing replacement trustees without the oversight of an interested board.

Keith Meister of Corvex and Jeff T. Blau of Related issued the following statement:

“We believe that the initiatives launched today present a clear and attractive path for shareholders of CWH to remove the current board of trustees and bring change to CWH. We are confident that ultimately they cannot get around the simple fact that CWH’s charter gives all shareholders the ability to remove the board by means of written consent with a two-thirds vote. In our view and that of our lawyers, any bylaw amendment that tries to make an end-run around this clear right is simply unenforceable.”

Corvex and Related have engaged Deutsche Bank Securities Inc. as their financial advisor in connection with their investment in CWH. Furthermore, Deutsche Bank has delivered a “highly confident letter” to Corvex and Related to the effect that, subject to the assumptions, terms and conditions described therein, Deutsche Bank is highly confident of its ability to arrange third party debt financing to replace the Company’s existing term loan and revolving credit agreement. Corvex and Related intend to work with Deutsche Bank on any further required financing in connection with their effort.

Additional Information Regarding the Consent Solicitation

In connection with their solicitation of written consents, Corvex Management LP and Related Fund Management, LLC have filed a preliminary written consent solicitation statement with the Securities and Exchange Commission (the “SEC”) to solicit written consents from shareholders of the Company. Investors and security holders are urged to read the preliminary written consent solicitation statement in its entirety, and the definitive written consent solicitation statement and other relevant documents when they become available, because they will contain important information regarding the consent solicitation. The preliminary and definitive written consent solicitation statement and all other relevant documents will be available, free of charge, on the SEC’s website at www.sec.gov.

The following persons are participants in connection with the written consent solicitation of the Company’s shareholders: Corvex Management LP, Keith Meister, Related Fund Management, LLC, Related Real Estate Recovery Fund GP-A, LLC, Related Real Estate Recovery Fund GP, LP, Related Real Estate Recovery Fund, LP, RRERF Acquisition, LLC, Jeff T. Blau and Richard O’Toole. Information regarding the participants in the consent solicitation and a description of their direct and indirect interests, by security holdings or otherwise, to the extent applicable, is available in the preliminary written consent solicitation statement filed with the SEC on March 13, 2013.

About Corvex Management LP

Corvex Management LP is an investment firm headquartered in New York, New York that engages in value-based investing across the capital structure in situations with identifiable catalysts. Corvex was founded in March 2011 and follows an opportunistic approach to investing with a specific focus on equity investments, special situations and distressed securities largely in North America.

About Related Fund Management, LLC

Related Fund Management, LLC is an affiliate of Related Companies, one of the most prominent privately-owned real estate firms in the United States. Formed 40 years ago, Related is a fully-integrated, highly diversified industry leader with experience in virtually every aspect of development, acquisitions, management, finance, marketing and sales. Related’s existing portfolio of real estate assets, valued at over $15 billion, is made up of best-in-class mixed-use, residential, retail, office and affordable properties. For more information about Related Companies please visit www.related.com.