I paid that taxes I thought I owed, however I found out that I would get a refund instead. Will I get the money I paid back along with my refund?

[92flamefist]

I paid the money I thought I owed when I filed for an extension.

[mesquitebean]

Have you already filed the return?   If so, in that return did you report the amount you paid with the extension request so that you get credit for it?  If you reported the extension payment, then it should already be accounted for in the return.

If you haven't filed yet,  we can tell you how to report the payment you made with the extension so that you get credit for it.

Or did you already file, but failed to report the extension payment?

[92flamefist]

I already file and didn't report the extension payment.

[mesquitebean]

Well, the IRS "might" catch it, but it may not be in time for your filed refund.  It's possible they send you a check for the overpayment, but it could take several weeks.

The other possibility is to file an amended tax return, but that takes 16 weeks to process anyway.   In any case, I would NOT file an amended return until you receive the refund that you are due from the return, and then decide what to do.

Once you receive the initial refund, I'm not sure which is the best approach--waiting to see if the IRS sends a second refund or  file an amended return (after receiving first refund) to report the extension payment.   I'll see if a tax person who may have seen these types of circumstances before can comment.

@TaxGuyBill  When you are next in the forum, are you able to suggest which approach is best in this circumstance?   Thanks.

[TaxGuyBill]

Usually the IRS does see the over payment and sends the additional refund, but it sometimes takes a while, and sometimes it gets lost and you need to call them to figure out what happened to it.

Personally, I would call the IRS and ask them.  It is likely that calling them will trigger them to 'see' it and send a refund, probably quicker than just waiting for it.

[mesquitebean]

Thank you @TaxGuyBill  That sounds like a good idea.

@92flamefist
 I'll leave an answer below that tells how to reach a live agent at the IRS so  you can advise them of your overpayment and see what they recommend.

[mesquitebean · Accepted solution]

See the above discussion and the advice from TaxGuyBill.  Hopefully, the IRS will notice the overpayment and simply provide the refund, but that can take several weeks.

In the meantime, to play it safe, you can phone the IRS and tell them what happened, and once brought to their attention, they may have additional advice or reassurance.

Here's how to maneuver through their phone tree to reach a live agent:

800-829-1040  hours 7 AM - 7 PM local time Mon-Fri

• First choose your language. Press 1 for English.
• Then do not choose the first choice re: "Refund", or it will send you to an automated phone line.
• Instead, press 2 for "personal income tax".
• Then press 1 for "form, tax history, or payment".  
• Then press 3 "for all other questions."
• Then press 2 "for all other questions."  It should then transfer you to an agent, but there is likely to be a long wait.

I usually use a speaker phone so I can work on something else.