SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D/A

(Rule 13d-101)

Under the Securities Exchange Act of 1934

(Amendment No. 2)

(Name of Issuer)

(Title of Class of Securities)

(CUSIP NUMBER)

(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 which is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f) or 13d-1(g) check the following box ¨

The information required in 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, as amended (the “Act”), or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act.

13D/A

* SEE INSTRUCTIONS BEFORE FILLING OUT

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13D/A

* SEE INSTRUCTIONS BEFORE FILLING OUT

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13D/A

* SEE INSTRUCTIONS BEFORE FILLING OUT

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AMENDMENT NO. 2 TO SCHEDULE 13D

This Amendment No. 2 to Schedule 13D (this “Amendment”) is being filed on behalf of (i) Paragon Associates and Paragon Associates II Joint Venture, a joint venture (“Paragon JV”) formed by Paragon Associates, Ltd., a Texas limited partnership (“Paragon”) and Paragon Associates II, Ltd. a Texas limited partnership (“Paragon II”), (ii) Bradbury Dyer III / SJ Madstone LP, a Texas limited partnership (“Madstone”) and (iii) Bradbury Dyer III (“Mr. Dyer”, and together with Paragon JV and Madstone, the “Reporting Persons”), relating to shares of common stock, $0.001 par value (the “Common Stock”) of The Spectranetics Corporation, a Delaware corporation (the “Issuer”). This Amendment modifies the original Schedule13D filed on November 2, 2010 (the “Original 13D”), which has been previously modified by Amendment No. 1 to the Original 13D on May 17, 2011.

This Amendment relates to (i) Common Stock purchased by Mr. Dyer for the account of Paragon JV on behalf of Paragon and Paragon II. Mr. Dyer, as the authorized agent to Paragon JV, controls the investment decisions of Paragon JV and (ii) Common Stock purchased by Madstone, for which Mr. Dyer serves as the general partner.

Item 3 of the Original 13D is hereby amended and restated as below:

The net investment costs (including commissions, if any) of the shares of Common Stock purchased by the Reporting Persons is $10,062,210. The source of these funds was the working capital of the Reporting Persons.

Item 5 of the Original 13D is hereby amended and restated as below:

34,580,631 shares of Common Stock were outstanding as of August 2, 2012, based upon the Issuer’s Form 10-Q filed with the Securities and Exchange Commission on August 7, 2012.

(ii) As of August 17, 2012, Mr. Dyer beneficially owns 1,935,736 shares of Common Stock held by Paragon JV. Mr. Dyer does not have direct beneficial ownership of the 1,935,736 shares of the Issuer’s Common Stock held by Paragon JV; however, Mr. Dyer, as the general partner of Paragon I and Paragon II, as agent for Paragon JV, may be deemed, for purposes of determining beneficial ownership pursuant to Rule 13d-3, to have shared beneficial ownership of such shares. These 1,935,736 shares of Common Stock represent 5.6% of the Issuer’s outstanding shares of Common Stock.

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(ii) Mr. Dyer, as the authorized agent of Paragon JV, has the shared power to vote and dispose of the 1,935,736 shares of Common Stock held by Paragon JV.

(c) Transactions in the Issuer’s securities by the Reporting Persons during the last sixty days are listed in Annex A attached hereto.

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SIGNATURES

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

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Annex A

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