How do I fix an old excess HSA contribution on my federal tax return?
So back in 2019 I retired earlier than planned (health reasons unfortunately) and there was some confusion with my former employer's payroll department. They ended up making a small contribution of $127 to my HSA in January 2020, after I was no longer eligible since I didn't have an HDHP anymore. When I filed my 2020 taxes in 2021, TurboTax flagged this as an excess contribution. I remember seeing something about it but honestly I was dealing with some medical stuff at the time and completely forgot to address it. Now I'm getting ready for this year's taxes and realized I never fixed this issue! I know there's a 6% excise tax on excess contributions, but I'm confused about how to handle this now, three tax seasons later. Do I need to file amended returns for multiple years? Is there a way to just fix it on this year's return? I still have the HSA account but haven't touched that money. Any advice on the simplest way to resolve this without getting into trouble with the IRS would be really appreciated. I feel stupid for letting this slip through the cracks for so long!
21 comments


Finley Garrett
The good news is that you can still fix this! When you have an excess HSA contribution from a previous year, you have a couple of options. The cleanest approach is to contact your HSA provider and request a "removal of excess contribution" specifically for that $127. Make sure to tell them it was an excess contribution for tax year 2020. They'll withdraw not just the excess amount but also any earnings attributed to that excess portion. They'll issue you a corrected Form 5498-SA showing the proper contribution amount and you'll likely receive a 1099-SA for the withdrawal. Yes, you'll owe the 6% excise tax for each year the excess remained in your account (2020, 2021, 2022, and 2023), which you'll report using Form 5329 for each of those years. You don't necessarily need to file complete amended returns - you can just file Form 5329 separately for the previous years along with payment for the excise tax (about $7.62 per year). Going forward, it's worth doing a quick annual check that your HSA contributions align with your eligibility status, especially around employment changes.
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Madison Tipne
•Thanks for this clear explanation! Question: if they remove the excess contribution now, does that mean the 1099-SA will be issued for 2024 tax year even though the excess contribution was from 2020? And do you report the earnings as income in 2024 or would that also need to be reported on amended returns?
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Finley Garrett
•The 1099-SA will be issued for the tax year in which you actually remove the excess contribution, so in this case 2024 if you do it now. The earnings attributed to the excess amount will be reported as "other income" on your 2024 tax return, not on amended returns. This is actually a benefit of the system - you only have to deal with the earnings in the current year rather than amending multiple years of returns. The 6% excise tax on Form 5329 is the only thing you need to handle for the previous years.
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Holly Lascelles
I had a similar situation last year with an HSA excess contribution that was even smaller than yours (about $85). I spent weeks trying to navigate the IRS documentation and was getting nowhere. I eventually found this service called taxr.ai (https://taxr.ai) that was surprisingly helpful. I uploaded my HSA statements and tax documents, and it identified exactly what forms I needed to file and even showed me how to fill them out. The nice thing was that it walked me through the process of handling multiple tax years with this excess contribution issue - something that was really confusing me before. It specifically helped me understand how to complete the Form 5329 correctly for each affected year, which was a huge relief.
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Malia Ponder
•Did you have to file amended returns for every year the excess contribution was in your account? That's what I'm dreading about my situation - having to redo multiple years of tax returns.
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Kyle Wallace
•I've been thinking about trying one of these AI tax tools. Was it actually accurate? I've heard horror stories about tax software giving wrong advice for specialized situations.
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Holly Lascelles
•You don't need to file complete amended returns, just Form 5329 for each affected year. The tool helped me realize I could file this form by itself which saved a ton of headache - no need to redo entire tax returns. The information was spot-on for my HSA issue. What impressed me was that it actually cited specific IRS publications and rules rather than giving generic advice. For something this specific (excess HSA contributions), it really knew the details. I double-checked with the IRS publications it referenced and everything matched up.
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Malia Ponder
Just wanted to follow up and say I ended up trying taxr.ai after reading about it here! It was actually super helpful for my HSA excess contribution situation. I uploaded my HSA statements and it immediately identified the excess amount and calculated the 6% excise tax I owed for each year. The best part was that it generated the Form 5329 for each year I needed to file and gave step-by-step instructions for submitting them without having to amend my entire returns. It also explained exactly what to tell my HSA administrator when requesting the removal of excess contributions. Saved me a ton of time and definitely reduced my anxiety about dealing with the IRS over this. Just got confirmation that my excess contribution issue is resolved!
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Ryder Ross
I had a nightmare trying to reach the IRS about my HSA issue last year. Spent literally hours on hold only to get disconnected. After the third attempt, I was about to give up when another tax forum recommended this service called Claimyr (https://claimyr.com). They have a demo of how it works here: https://youtu.be/_kiP6q8DX5c Basically, they hold your place in the IRS phone queue and call you when an agent picks up. I was super skeptical, but I was desperate after wasting so much time on hold. Used them and got a call back with an actual IRS agent on the line within about 45 minutes while I was just going about my day. The agent was able to tell me exactly how to handle my excess HSA contribution from years ago and confirmed I only needed to file Form 5329 for the affected years without doing full amended returns. Huge relief to get official confirmation.
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Gianni Serpent
•How does this actually work? Do they just sit on hold for you? And are you sure the person on the other end was actually from the IRS? Sounds a bit sketchy to me.
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Henry Delgado
•Yeah right. No way this actually works. The IRS phone system is deliberately designed to be impossible to navigate. I'll believe it when I see it.
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Ryder Ross
•They use an automated system that holds your place in the phone queue and then calls you when it detects a human has answered. You're connected directly to the IRS agent - Claimyr isn't in the middle of your conversation with the IRS at all. Definitely a real IRS agent. They verified my identity using the standard IRS verification process once I was connected, and they had access to all my tax records. I even called the official IRS number afterwards to confirm, and yes, it's legit. The service just handles the hold time, not the actual call with the IRS.
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Henry Delgado
Alright, I have to eat my words. After being completely skeptical about Claimyr, I decided to try it as a last resort because I was getting nowhere with the IRS hotline about my HSA issue. I'm shocked to say it worked exactly as advertised. I signed up, entered my number, and went back to work. About an hour later my phone rang and there was an actual IRS agent on the line. Not a scam, not a third party - a legitimate IRS employee who helped me resolve my excess contribution problem. They confirmed I only needed to file Form 5329 for each year the excess was in my account, and explained exactly how to calculate the earnings portion. Saved me hours of frustration and probably a mistake or two on the forms. Sometimes being proven wrong is actually a good thing!
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Olivia Kay
I'm a bit confused about the 6% excise tax on excess HSA contributions. Is that 6% of just the excess amount ($127 in your case) or 6% of your entire HSA contribution for the year? And do you pay that penalty every year until you fix it?
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Joshua Hellan
•It's 6% of just the excess amount, not your entire contribution. And yes, you pay it for every year the excess remains in your account, which is why it's best to fix it ASAP once you discover the problem. In OP's case, that's about $7.62 per year.
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Olivia Kay
•Thanks for clarifying! That's not as bad as I thought then. I was worried it would be 6% of the entire HSA contribution which could be thousands of dollars.
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Jibriel Kohn
Has anyone actually done the "removal of excess contributions" process with their HSA administrator? My HSA is with HealthEquity and their customer service is terrible. Wondering if I should just pay the 6% tax for a couple years rather than deal with them...
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Edison Estevez
•I did this with Fidelity HSA last year and it was pretty straightforward. Just called, told them I needed to remove an excess contribution from tax year 2022, and they had a specific form for it. Took about 10 minutes on the phone and then a week to process.
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Chloe Anderson
Don't beat yourself up about this - medical issues can definitely make it hard to stay on top of everything! The good news is that while you'll owe some penalty, it's really not that bad in your case. For a $127 excess contribution, you're looking at about $7.62 per year in excise tax (6% of $127). So for 2020-2023, that's roughly $30 total - definitely manageable. Here's what I'd recommend: First, call your HSA administrator and request removal of the excess contribution from 2020. They should be able to calculate any earnings on that $127 and remove both the excess and earnings. You'll get a 1099-SA for 2024 showing the withdrawal. Then file Form 5329 for each year 2020-2023 to pay the 6% excise tax. You don't need to amend your full returns - just file the 5329 forms separately with payment. The earnings portion will be taxable income on your 2024 return, but since it's been sitting there for years, it might actually be a decent amount that's been growing tax-free. One tip: when you call your HSA administrator, be very specific that you want to "remove excess contributions for tax year 2020" - use those exact words. Some customer service reps get confused if you just say you want to withdraw money.
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StarSeeker
I went through something very similar last year! Had an excess HSA contribution from 2019 that I didn't catch until 2023. The key thing to remember is that you're not in any serious trouble - this happens more often than you'd think, especially during job transitions. Here's what worked for me: I called my HSA provider (mine was with HSA Bank) and specifically asked for "removal of excess contribution for tax year 2020." They knew exactly what I was talking about and handled it within about a week. They removed both the $127 excess and any earnings attributed to it. The 6% excise tax isn't too painful on such a small amount - you're looking at about $7.62 per year, so maybe $30-35 total for all the years it's been sitting there. I filed Form 5329 for each affected year separately (didn't need to amend full returns) and just sent payment with each form. The earnings that get removed will show up as income on your 2024 return, but honestly after sitting in the HSA for 4+ years, there might be a nice little growth there that partially offsets the penalties. Don't stress too much about this - you're being proactive now and that's what matters. The IRS deals with HSA issues all the time and as long as you're making the effort to fix it, they're pretty reasonable about these situations.
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Liam Cortez
•This is really reassuring to hear from someone who went through the exact same thing! I'm curious - when you filed the Form 5329 for each year, did you have to mail them separately or could you bundle them together? And did you end up owing any interest on the excise tax payments since they were technically late? Also, you mentioned the earnings might have grown nicely over the 4+ years - did that end up being the case for you? I'm wondering if the growth might actually offset some of the penalty costs, which would make this whole situation a bit less painful.
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