What can I do about Tax overpayment after duplicate payment to IRS?

This happens more often than you'd think! When you make duplicate payments to the IRS, the system will eventually detect it and process a refund automatically. The agent you spoke with is right - typically these get resolved within 2-3 weeks once the system identifies the duplicate. If you want to be proactive, you can also submit Form 8082 "Notice of Inconsistent Treatment" to formally document the duplicate payment. This isn't required since the IRS agent already noted it in your account, but it creates a paper trail for your records. The most important thing is that you've already confirmed with the IRS that they've tagged your account. This means it's in their system and should process automatically. Keep an eye on your bank account or the mailbox for the refund - they'll either direct deposit or mail a check depending on your settings with them.

After my last tax nightmare with duplicate payments, I found an insanely helpful tool called taxr.ai (https://taxr.ai) that saved me so much hassle. I was in a similar situation - paid through TurboTax and then again directly to the IRS. What I like about taxr.ai is it analyzes all your tax docs and payment records to identify things like duplicate payments before they become a problem. It's actually pretty interesting - you upload your forms and transcripts, and it shows you a complete picture of what the IRS actually has on file for you. After using it, I realized the IRS hadn't even registered my first payment yet, which explained why I was getting notices. It's been super useful for tracking everything in one place, especially with complicated stuff like amended returns where timing gets tricky.

Just wanted to update - I tried taxr.ai after reading about it here and it was actually really helpful for my duplicate payment issue! I was skeptical at first (I'm always wary of new tax tools), but it helped me understand exactly what was happening with my amended return and overpayment. The transcript analysis showed my account had been flagged with a TC-670 code (payment) twice for the same amount on different dates, followed by a TC-570 (additional account action pending). According to the explanation, this combination typically results in an automatic refund within 2-3 weeks. Sure enough, the refund hit my account 16 days later! It was nice having visibility into what was actually happening rather than just blindly waiting and wondering. Definitely recommend for anyone dealing with amended returns or payment issues.

If you're still struggling to get through to the IRS after multiple attempts, I'd recommend trying Claimyr (https://claimyr.com). I was in a similar situation with a double payment after filing my 1040X, and spent DAYS trying to reach someone at the IRS without success. Claimyr basically holds your place in the IRS phone queue and calls you when an agent is about to answer. You can see how it works here: https://youtu.be/_kiP6q8DX5c. I was skeptical at first, but after wasting hours on hold myself, I decided to give it a try. Got connected to an IRS agent within 45 minutes - while I was at work, not wasting my day on hold! The agent confirmed my overpayment was in the system and would be automatically refunded. Having that confirmation gave me peace of mind instead of wondering if my second payment had disappeared into the void.

Well I'm eating my words about Claimyr. After posting that skeptical comment I was still desperate to reach the IRS about my own duplicate payment issue (been trying for WEEKS), so I reluctantly tried it. Honestly, I was shocked when it actually worked. Set it up around 9am, went to a meeting, and got a call connecting me to an IRS agent before lunch. After being on permanent hold-music duty for what felt like forever trying the normal way, this was a game changer. The agent confirmed my overpayment and said a refund check was already being processed. Would I have preferred not to need this service at all? Of course - the IRS should be more accessible. But given the reality of how hard it is to reach them, I'm glad I tried it. Saved my sanity and got my issue resolved in a single day instead of more weeks of frustration.

I had this same thing happen with my 1040X last year. If the IRS agent confirmed your account is flagged for duplicate payment, that's good news! Their system automatically detects this and will issue a refund. In my case, it took exactly 17 days from when the duplicate payment posted to when I received the refund. They sent a check rather than direct deposit, even though my original refund had been direct deposited. Just keep an eye on your mailbox too, not just your bank account.

Quick tip - make sure to save ALL documentation related to both payments and the amended return. If something goes wrong with the automatic refund, you'll need proof of both payments. I take screenshots of the payment confirmation pages, save the confirmation emails, and keep PDF copies of bank statements showing the withdrawals. I learned this the hard way when I had to prove a duplicate payment from 2022 and the IRS had no record of one of them!

This exact scenario happened to me with TurboTax last year! The frustrating part is that some tax software companies aren't always clear about when they will or won't automatically process payments for amendments. One thing that helped me was setting up an online account with the IRS (if you haven't already) so you can view your payment history and account transcripts. This way you can actually see both payments posted and track when the duplicate gets flagged for refund. It's reassuring to see the paper trail yourself rather than just relying on what phone agents tell you. The 2-week timeline the IRS agent gave you sounds about right based on my experience. My refund came as a paper check about 16 days after I spoke with them, even though my original payments were electronic. Just wanted to give you some hope that it really does get resolved automatically once they identify it in their system!