As filed with the Securities and Exchange Commission on September 16, 2014

Registration No. 333-197660

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

AMENDMENT NO. 3 TO

FORM S-1

REGISTRATION STATEMENT

UNDER

THE SECURITIES ACT OF 1933

VIRGIN AMERICA INC.

(Exact name of registrant as specified in its charter)

555 Airport Boulevard

Burlingame, California 94010

(650) 762-7000

(Address, including zip code, and telephone number, including

area code, of registrant’s principal executive offices)

C. David Cush

President and Chief Executive Officer

Virgin America Inc.

555 Airport Boulevard, Burlingame, California 94010

(650) 762-7000

(Name, address, including zip code, and telephone number, including area code, of agent for service)

Copies To:

Approximate date of commencement of the proposed sale to the public:

As soon as practicable after this Registration Statement becomes effective.

If any of the securities being registered on this Form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, check the following box. ¨

If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ¨

If this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ¨

If this Form is a post-effective amendment filed pursuant to Rule 462(d) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ¨

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.

CALCULATION OF REGISTRATION FEE

The Registrant hereby amends this Registration Statement on such date or dates as may be necessary to delay its effective date until the Registrant shall file a further amendment which specifically states that this Registration Statement shall thereafter become effective in accordance with Section 8(a) of the Securities Act of 1933 or until the Registration Statement shall become effective on such date as the Commission, acting pursuant to said Section 8(a), may determine.

EXPLANATORY NOTE

This Amendment No. 3 to Form S-1 Registration Statement (Registration No. 333-197660) of Virgin America Inc. is being filed solely to include exhibits to the Registration Statement not previously filed. Accordingly, Part I, the form of prospectus, has been omitted from this filing.

PART II

The following table sets forth the costs and expenses, other than underwriting discounts, payable in connection with the sale and distribution of the securities being registered. All amounts are estimated except the SEC registration fee and the FINRA filing fee. All the expenses below will be paid by Virgin America.

Virgin America Inc. is a Delaware corporation. Section 145 of the Delaware General Corporation Law authorizes a court to award, or a corporation’s board of directors to grant, indemnity to directors and officers in terms sufficiently broad to permit such indemnification under certain circumstances for liabilities, including reimbursement for expenses incurred, arising under the Securities Act of 1933, as amended. Our amended and restated certificate of incorporation to be in effect upon the completion of this offering provides for indemnification of our directors, officers, employees and other agents to the maximum extent permitted by the Delaware General Corporation Law, and our amended and restated bylaws to be in effect upon the completion of this offering provide for indemnification of our directors, officers, employees and other agents to the maximum extent permitted by the Delaware General Corporation Law. In addition, we have entered into indemnification agreements with our directors, officers and some employees containing provisions which are in some respects broader than the specific indemnification provisions contained in the Delaware General Corporation Law. The indemnification agreements may require us, among other things, to indemnify our directors against certain liabilities that may arise by reason of their status or service as directors and to advance their expenses incurred as a result of any proceeding against them as to which they could be indemnified. Reference is also made to Section      of the underwriting agreement to be filed as Exhibit 1.1 hereto, which provides for indemnification by the underwriters of our officers and directors against certain liabilities.

During the last three years, the Company made sales of the following unregistered securities:

Warrant Agreements

In December 2011, the Company entered into warrant agreements with the Virgin Group and Cyrus Capital, pursuant to which it granted to the Virgin Group and Cyrus Capital warrants to purchase an aggregate of 19,250,000 shares of Virgin America common stock at an exercise price of $3.50 per share. The warrants expire in December 2041 and are only exercisable after they have been transferred in specified circumstances (provided

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that any exercise thereafter would not violate any U.S. statute or regulation concerning the ownership and control of a U.S. airline by non-U.S. citizens), or in connection with the settlement of such warrants to an underwriter in connection with a public offering.

In November 2012, the Company entered into warrant agreements with Frederick Reid, who served as the Company’s first Chief Executive Officer until December 2007, and Joyce Reid, his spouse, pursuant to which the Company granted to them warrants to purchase an aggregate of 175,000 shares of common stock at an exercise price of $5.00 per share and warrants to purchase an aggregate of 550,000 shares of common stock at an exercise price of $10.00 per share. Half of the shares under each of these warrants vested immediately, and the other half vests upon the occurrence of a liquidity event, including a public offering, subject to certain conditions. The warrants expire on January 12, 2040 or immediately after the earlier closing of a liquidity event, including a public offering, and are exercisable only upon the occurrence of a liquidity event, including a public offering, provided that any exercise would not violate any U.S. statute or regulation concerning the ownership and control of a U.S. airline by non-U.S. citizens.

In May 2013, in connection with the cancellation of a portion of the Company’s then outstanding related-party debt, the Company entered into warrant agreements with the Virgin Group and Cyrus Capital pursuant to which it granted (i) warrants to purchase an aggregate of 12,244,558 shares of Virgin America common stock at an exercise price of $2.50 per share to Cyrus Capital, (ii) warrants to purchase an aggregate of 155,455,440 shares of Virgin America common stock at an exercise price of $2.50 per share to the Virgin Group, and (iii) warrants to purchase an aggregate of 7,446,931 shares of Virgin America common stock at an exercise price of $0.01 per share to the Virgin Group. The warrants expire in May 2043 and are only exercisable after they have been transferred in specified circumstances (provided that any exercise thereafter would not violate any U.S. statute or regulation concerning the ownership and control of a U.S. airline by non-U.S. citizens) or in connection with the settlement of such warrants to an underwriter in connection with a public offering.

Note Purchase Agreements

In December 2011, the Company issued $150.0 million of senior secured notes to the Virgin Group and Cyrus Capital. In May 2013, the Virgin Group transferred the notes it acquired to Cyrus Capital. The notes purchased bear interest at a rate of 17.0% per annum, of which 8.5% is payable quarterly in arrears, and 8.5% is compounded annually. The principal and accrued interest on the notes become due on June 9, 2016 if not earlier repaid or redeemed. The notes are redeemable at the Company’s option at any time and at the lenders’ option upon a change of control or certain qualified sales. The Company is also required to redeem the notes upon the incurrence of any senior debt. The notes are secured by substantially all of the Company’s assets.

In May 2013, the Company issued $75.0 million of senior secured notes to the Virgin Group and Cyrus Capital. The notes bear interest at a rate of 17.0% per annum, compounded annually. The principal and accrued interest on the notes become due on June 9, 2016 if not earlier repaid or redeemed. The notes are redeemable at the Company’s option at any time and at the lenders’ option upon a change of control or certain qualified sales. The Company is also required to redeem the notes upon the incurrence of any senior debt. The notes are secured by substantially all of the Company’s assets.

Equity Awards

Since January 1, 2011, the Company issued and sold an aggregate of 8,742 shares of common stock upon the exercise of options issued to directors, officers, employees, consultants and service providers under the Company’s 2005 Stock Incentive Plan at a weighted-average exercise price of $1.81 per share for aggregate cash consideration of approximately $15,800.

Since January 1, 2011, the Company granted options to directors, officers, employees, consultants and service providers under the 2005 Stock Incentive Plan with respect to an aggregate of 7,064,760 shares of common stock, at a weighted-average exercise price of $2.01 per share.

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Since January 1, 2011, the Company granted to its directors, officers, employees, consultants and other service providers an aggregate of 2,413,200 RSUs to be settled in shares of common stock under the Company’s 2005 Stock Incentive Plan.

Since January 1, 2011, the Company granted to its directors, including its chief executive officer, an aggregate of 3,396,432 RSUs to be settled in shares of common stock outside of the Company’s 2005 Stock Incentive Plan.

The Company’s board of directors has approved, contingent upon the consummation of the transactions contemplated by the 2014 Recapitalization, the grant to certain executive officers and other members of management of an aggregate of 1,650,000 RSUs, which will vest immediately and will be settled in shares of common stock under the Company’s 2005 Stock Incentive Plan.

Unless otherwise stated, the sales of the above securities were deemed to be exempt from registration under the Securities Act in reliance upon Sections 3(a)(9) or 4(a)(2) of the Securities Act or Regulation D or Regulation S promulgated thereunder, or Rule 701 promulgated under Section 3(b) of the Securities Act as transactions by an issuer not involving any public offering or pursuant to benefit plans and contracts relating to compensation as provided under Rule 701. The recipients of the securities in each of these transactions represented their intentions to acquire the securities for investment only and not with a view to or for sale in connection with any distribution thereof, and appropriate legends were placed upon the stock certificates issued in these transactions. All recipients had adequate access, through their relationships with Virgin America, to information about Virgin America.

There were no underwriters employed in connection with any of the transactions set forth in Item 15.

See the Exhibit Index, which follows the signature pages hereto and is incorporated herein by reference.

The undersigned registrant hereby undertakes that:

(1) for purposes of determining any liability under the Securities Act, the information omitted from the form of prospectus filed as part of this registration statement in reliance upon Rule 430A and contained in a form of prospectus filed by the registrant pursuant to Rule 424(b)(1) or (4) or 497(h) under the Securities Act shall be deemed to be part of this registration statement as of the time it was declared effective;

(2) for the purpose of determining any liability under the Securities Act, each post-effective amendment that contains a form of prospectus shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof;

(3) for the purpose of determining liability of the registrant under the Securities Act to any purchaser in the initial distribution of the securities, the undersigned registrant undertakes that in a primary offering of securities of the undersigned registrant pursuant to this registration statement, regardless of the underwriting method used to sell the securities to the purchaser, if the securities are offered or sold to such purchaser by means of any of the following communications, the undersigned registrant will be a seller to the purchaser and will be considered to offer or sell such securities to such purchaser:

(i) any preliminary prospectus or prospectus of the undersigned registrant relating to the offering required to be filed pursuant to Rule 424;

(ii) any free writing prospectus relating to the offering prepared by or on behalf of the undersigned registrant or used or referred to by the undersigned registrant;

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(iii) the portion of any other free writing prospectus relating to the offering containing material information about the undersigned registrant or its securities provided by or on behalf of the undersigned registrant; and

(iv) any other communication that is an offer in the offering made by the undersigned registrant to the purchaser; and

(4) the undersigned will provide to the underwriters at the closing specified in the underwriting agreement, certificates in such denominations and registered in such names as required by the underwriters to permit prompt delivery to each purchaser.

Insofar as indemnification for liabilities arising under the Securities Act may be permitted to directors, officers and controlling persons of the registrant pursuant to the provisions described in Item 14, or otherwise, the registrant has been advised that in the opinion of the Securities and Exchange Commission such indemnification is against public policy as expressed in the Securities Act and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the registrant of expenses incurred or paid by a director, officer or controlling person of the registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, the registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of such issue.

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SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, as amended, we have duly caused this Registration Statement on Form S-1 to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of Burlingame, State of California, on the 16th day of September, 2014.

Pursuant to the requirements of the Securities Act of 1933, as amended, this Registration Statement has been signed by the following persons in the capacities and on the dates indicated.

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EXHIBIT INDEX