SECOND AMENDED AND RESTATED SECURED PROMISSORY NOTE (Loan A)

Exhibit 4.6

SECOND AMENDED AND RESTATED SECURED PROMISSORY NOTE

(Loan A)

FOR VALUE RECEIVED, the undersigned, XTERA COMMUNICATIONS, INC., a Delaware corporation (“Borrower”), HEREBY PROMISES TO PAY to HORIZON FUNDING TRUST 2013-1, as assignee of HORIZON TECHNOLOGY FINANCE CORPORATION, a Delaware corporation (“Lender”) the principal amount of Ten Million and 00/100 Dollars ($10,000,000.00) or such lesser amount as shall equal the outstanding principal balance of the Loan A made to Borrower by Lender pursuant to the Loan Agreement (as defined below), and to pay all other amounts due with respect to the Loan on the dates and in the amounts set forth in the Loan Agreement. This Note replaces and supersedes, in its entirety, that certain Amended and Restated Secured Promissory Note (Loan A) issued by Borrower to Lender on April 1, 2013 (the “Original Note”). Nothing contained herein shall be deemed a repayment or novation of the Original Note.

Interest on the principal amount of this Note from the date of this Note shall accrue at the Loan Rate or, if applicable, the Default Rate. The Loan Rate for this Note is 11.50% per annum based on a year of twelve 30-day months. If the Funding Date is not the first day of the month, interim interest accruing from the Funding Date through the last day of that month shall be paid on the first calendar day of the next calendar month. Commencing July 1, 2011, through and including June 1, 2012, on the first day of each month (each an “Initial Interest Payment Date”) Borrower shall make payments of accrued interest only on the outstanding principal amount of the Loan in the amount of Ninety-Five Thousand Eight Hundred Thirty-Three and 33/100 Dollars ($95,833.33). Commencing on July 1, 2012, and continuing on the first day of each month thereafter through March 1, 2013 (each an “Initial Principal and Interest Payment Date”), Borrower shall make to Lender a payment of principal plus accrued interest on the then outstanding principal amount due hereunder each in the amount of Three Hundred Eighty-Five Thousand One Hundred Twenty-Six and 65/100 Dollars ($385,126.65). Commencing on April 1, 2013, through and including June 1, 2013 on the first day of each month (each a “Subsequent Interest Payment Date”), Borrower shall make a payment of accrued interest only on the outstanding principal amount of the Loan in the amount of Sixty-Nine Thousand Nine Hundred Three and 61/100 Dollars ($69,903.61). Commencing on July 1, 2013, through and including September 1, 2013 on the first day of each month (each a “Partial Principal and Interest Payment Date”), Borrower shall make payments of principal plus accrued interest on the then outstanding principal amount due hereunder in the amount of Two Hundred Twenty-Seven Thousand Five Hundred Fifteen and 13/100 Dollars ($227,515.13). On October 1, 2013 (the “Subsequent Principal and Interest Payment Date”), Borrower shall make to Lender a payment of principal plus accrued interest on the then outstanding principal amount due hereunder each in the amount of Four Hundred Fourteen Thousand One Hundred Twenty-Seven and 52/100 Dollars ($414,127.52). Commencing on November 1, 2013, through and including February 1, 2014 (each an “Additional Interest Payment Date”), on the first day of each month, Borrower shall make payments of accrued interest only on the outstanding principal amount of the Loan in the

amount of Sixty-One Thousand Nine Hundred Eighty-Six and 06/100 Dollars ($61,986.06). Commencing as of March 1, 2014, and continuing on the first day of each month thereafter (each, an “Additional Principal and Interest Payment Date”, and together with the Initial Interest Payment Dates, the Initial Principal and Interest Payment Dates, the Subsequent Interest Payment Dates, the Partial Principal and Interest Payment Dates, the Subsequent Principal and Interest Payment Date and the Additional Interest Payment Dates, the “Payment Dates”), Borrower shall make to Lender seventeen (17) equal payments of principal plus accrued interest on the then outstanding principal amount due hereunder each in the amount of Four Hundred Fourteen Thousand One Hundred Twenty-Seven and 52/100 Dollars ($414,127.52). On July 1, 2015, or the earlier repayment in full of the Loan, Borrower shall make a payment of One Million Four Hundred Sixty-Five Thousand Three Hundred Thirty-Three and 83/100 Dollars ($1,465,333.83) to Lender (the “Final Payment”). If not sooner paid, all outstanding amounts hereunder and under the Loan Agreement shall become due and payable on July 1, 2015.

Principal, interest and all other amounts due with respect to the Loan, are payable in lawful money of the United States of America to Lender as set forth in the Loan Agreement. The principal amount of this Note and the interest rate applicable thereto, and all payments made with respect thereto, shall be recorded by Lender and, prior to any transfer hereof, endorsed on the grid attached hereto which is part of this Note.

This Note is referred to in, and is entitled to the benefits of, the Venture Loan and Security Agreement dated May 10, 2011 by and between Borrower and Lender (as amended, the “Loan Agreement”). The Loan Agreement, among other things, (a) provides for the making of a secured Loan to Borrower, and (b) contains provisions for acceleration of the maturity hereof upon the happening of certain stated events.

This Note may not be prepaid except as set forth in Section 2.3 of the Loan Agreement.

This Note and the obligation of Borrower to repay the unpaid principal amount of the Loan, interest on the Loan and all other amounts due Lender under the Loan Agreement is secured under the Loan Agreement.

Presentment for payment, demand, notice of protest and all other demands and notices of any kind in connection with the execution, delivery, performance and enforcement of this Note are hereby waived.

Borrower shall pay all reasonable fees and expenses, including, without limitation, reasonable attorneys’ fees and costs, incurred by Lender in the enforcement or attempt to enforce any of Borrower’s obligations hereunder not performed when due. This Note shall be governed by, and construed and interpreted in accordance with, the laws of the State of Connecticut.

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IN WITNESS WHEREOF, Borrower has caused this Note to be duly executed by one of its officers thereunto duly authorized on the date hereof.

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