As specified in FAQ at NSDL e-GOV portal, 
If one person is having more than one PAN, the procedure for cancellation/surrender of one PAN is :-
“You may fill and submit PAN Change Request application form by mentioning the PAN which you are using currently on top of the form. All other PAN/s inadvertently allotted to you should be mentioned at item no. 11 of the form and the corresponding PAN card copy/s should be submitted for cancellation along with the form.”
But If you wish to cancel/ surrender your PAN (which you are currently using), then you need to visit your local Income Tax Assessing Officer with a request letter to cancel/ surrender your PAN.

The procedure for online cancellation/surrender of second PAN is :-

• Visit NSDL website.(https://www.protean-tinpan.com/)
• Click apply under Change/Correction in PAN Data.
• From the drop-down select the category ‘’ Changes or correction in existing PAN Card/ reprint of PAN Card (No changes in existing PAN Data)’’ option.
• After filling out the form, click on the ‘submit’ button. 
• One needs to keep in mind the token number for future references and continue with the process by clicking the’ Continue with PAN application form’ button.
• After clicking on the button of the ‘PAN application form’, you will be directed to the new webpage. On top of new webpage, select “submit scanned images with an option of e-sign.
• At the bottom-left on the page, one should mention details about the PAN Number that you want to retain.
• After that, the applicant needs to fill out the personal details including contact details and other details in the form.
• At the bottom of the next page,; the applicant needs to mention the details of additional PAN cards that he or she wants to surrender and then click on ‘Next Button’
• After that in the next screen, the applicant needs to select options such as identity proof, residence, and date of birth.
• The next step, after that, is uploading the scanned images of signature, required documents, and photographs.
• If an individual is requesting PAN Card surrender, then, in that case, the individual needs to sign the acknowledgment receipt or it must be signed by authorized signatories. 
• Review the application, after submitting the details. Before making payment, verification of details needs to be done.
• After doing verification of the details, the applicant needs to make the payment via credit card, debit card or internet banking.
• After the applicant makes a successful payment, acknowledgment of the same will be given to the applicant. Save and print the acknowledgment for future reference and as a proof of payment.
• Applicant after that, needs to send the acknowledgment to NSDL e- Gov along with the attachment of two photographs.
• On the envelope of ‘Acknowledgment copy, Title should be mentioned is ‘Application for PAN Cancellation’. Along with acknowledgement, the demand draft (if required) and the required documents (proof of an existing PAN (if any), proof of (identity, address and date of birth)) to NSDL.

You can download Designated centres accepting Online PAN documents. 
For more detail please visit https://www.protean-tinpan.com/

For holding more than one PAN, penalty of Rs. 10000/- may be imposed under section 272B. Hence immediately surrender the duplicate PAN to your AO. and please keep acknowledgement.