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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Form 10-K/A

(Amendment No. 2)

For the fiscal year ended December 31, 2012

or

COMMISSION FILE NUMBER 0-19871

STEMCELLS, INC.

(Exact name of Registrant as specified in its charter)

Registrant’s telephone number, including area code:

(510) 475-4000

Securities registered pursuant to Section 12(b) of the Act:

Securities registered pursuant to Section 12(g) of the Act:

None

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 a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

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

Aggregate market value of common stock held by non-affiliates at June 30, 2012: $20,259,263. Inclusion of shares held beneficially by any person should not be construed to indicate that such person possesses the power, direct or indirect, to direct or cause the direction of management policies of the registrant, or that such person is controlled by or under common control with the Registrant.

Common stock outstanding at October 4, 2013: 54,971,174 shares.

Documents incorporated by reference:

None

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Year 2012 Form 10-K/A Annual Report

EXPLANATORY NOTE

StemCells, Inc. (the “Company”) is filing this Amendment No. 2 (this “Amendment”) to its Annual Report on Form 10-K for the fiscal year ended December 31, 2012 (the “Form 10-K”) in response to comments received from the Securities and Exchange Commission (the “SEC”) regarding a request for confidential treatment of certain portions of Exhibit 10.34 (Loan and Security Agreement (the “Security Agreement”)), dated as of April 8, 2013, between the Company and Silicon Valley Bank (“SVB”), Exhibit 10.35 (Loan Agreement (the “Loan Agreement”)), dated as of April 9, 2013 between the Company and the California Institute for Regenerative Medicine (“CIRM”) and Exhibit 10.36 (Notice of Loan Award (the “Notice”)), dated as of April 10, 2013, between the Company and CIRM, each originally filed with Amendment No. 1 to the Form 10-K.

In response to SEC comments, this Amendment is being filed solely to file revised Exhibits 10.34, 10.35 and 10.36 to disclose such additional information in the Security Agreement, Loan Agreement and Notice as agreed upon with the SEC. Certain portions of Exhibits 10.34, 10.35, and 10.36 remain omitted in accordance with a request for confidential treatment that the Company has submitted to the SEC.

Each of Exhibits 10.34, 10.35 and 10.36 filed with this Amendment supersedes in its entirety the version of Exhibits 10.34, 10.35 and 10.36, respectively, previously filed with the Form 10-K.

This amendment does not affect any other items in our Original Report. Because no financial statements are contained in this amendment, we are not including certifications under section 906 of the Sarbanes-Oxley Act of 2002.

Notes regarding certain references

Except as otherwise expressly stated herein, this amendment continues to speak as of the date of the Original Report and we have not updated the disclosure contained in the Original Report or this amendment to reflect events that have occurred since the filing of the Original Report. Accordingly, this amendment should be read in conjunction with our Original Report and our other filings made with the SEC subsequent to the filing of the Original Report.

Throughout this Form 10-K/A, the words “we,” “us,” “our,” and “StemCells” refer to StemCells, Inc., including our directly and indirectly wholly-owned subsidiaries. “Common stock” refers to the common stock of StemCells, Inc., $0.01 par value.

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PART IV

(b) Exhibits

The documents set forth below are filed herewith or incorporated by reference to the location indicated.

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SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this Amendment No.2 to be signed on its behalf by the undersigned, thereunto duly authorized.

Dated: October 11, 2013

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