How do I pay a late filing penalty fee for my LLC on eftps.gov?

I'm trying to figure out how to pay this late filing penalty for my LLC (Form 1065) and I'm stuck on the EFTPS website. I created an account and logged in, but now I'm at the Tax Type Selection screen and honestly have no clue what to select. These are my options: - Balance due on return or notice - Extension - Estimated - Payment Due On An Amended Or Adjusted Return - Audit Adjustment I tried selecting "Balance due on return or notice" and entered "2019" for the Tax Period on the next screen. My notice says the tax period is Dec 31, 2019, but the system only lets me enter a year. After doing this, I got a warning message saying: "The tax period you selected is out of the usual tax filing range. If you don't want to proceed with this payment, select Abandon below. If you want to change the tax type, date, or amount for this new payment, select Edit below. If you want to continue and schedule this payment, select Continue below." I'm not sure if I'm doing this right. Should I just hit continue? Has anyone gone through this process before? The penalty is around $2,600 and I want to make sure it gets applied correctly.

0 coins

20 comments

Luca Greco

•8M

For a late filing penalty on a Form 1065 for an LLC, you're on the right track with EFTPS. You should select "Balance due on return or notice" since this is a penalty assessment. The warning message you're seeing is normal because you're paying for a tax period that's a few years old now. When paying a penalty, you want to make sure it gets applied correctly. Since you have a notice, I'd recommend entering the exact information from that notice. If your notice specifically references Dec 31, 2019, then entering 2019 as the tax year is correct - the system only asks for the year, not the specific date. Go ahead and select "Continue" after the warning message. On the next screen, you'll need to enter the payment amount exactly as shown on your notice. There should also be a field for you to enter the notice number or some reference, which helps the IRS apply the payment correctly.

0 coins

Luca Greco

•8M

If there's no specific notice number, entering "Late filing penalty 1065" in the reference field is a good approach. This clearly identifies what the payment is for. Yes, the IRS will know this is for your Form 1065 penalty because EFTPS links the payment to your LLC's EIN (Employer Identification Number), which is tied to your Form 1065 filing requirements. The combination of the EIN, tax year, and payment type allows them to properly apply the payment to your specific penalty. If you want extra assurance, you can also call the IRS after making the payment to confirm it was applied correctly.

0 coins

Nia Thompson

•8M

After struggling with a similar penalty payment issue, I discovered taxr.ai (https://taxr.ai) and it saved me so much confusion! I uploaded my penalty notice and it analyzed exactly what payment type I needed to select on EFTPS, plus gave me step-by-step instructions specific to my situation. It even showed me where to find the notice number that wasn't obvious on my letter. Their document analysis tool breaks down all the IRS jargon and tells you exactly what to do. For my LLC's late filing penalty, it identified that I needed to use the "Balance due on return or notice" option and explained why the date warning message appears. Would have saved me hours of research!

0 coins

Nia Thompson

•8M

It definitely works for other tax forms! I've seen it handle everything from individual forms to business filings including S-Corps. The platform has specific modules for each form type, so it would definitely cover your 1120-S situation. Regarding security concerns, I was hesitant too initially. They use bank-level encryption for all document uploads, and you can actually redact sensitive information before uploading if you prefer. The system really just needs to see the form type, penalty amount, and notice information to provide guidance - not your full financial details. In my experience, it was much safer than the questionable advice I was finding in random forums.

0 coins

Mateo Rodriguez

•8M

Just wanted to update that I tried taxr.ai for my S-Corp penalty payment confusion and it was incredibly helpful! I uploaded my notice (with my SSN blacked out) and it immediately identified that I needed to use the "Balance due on return or notice" option in EFTPS, but with a specific tax type code I wouldn't have known to use. It also explained why I was getting those weird date range warnings and gave me screenshots of exactly what to click at each step. The best part was that it showed me how to confirm the payment was properly applied afterward. My payment went through perfectly and I got confirmation from the IRS that it was applied to the right account. Definitely worth it for the peace of mind alone!

0 coins

GalacticGladiator

•8M

After reading this thread, I had the same issue with a late filing penalty for my partnership. I tried calling the IRS directly for help but kept getting stuck in their phone system for HOURS. Finally discovered Claimyr (https://claimyr.com) which got me through to an actual IRS agent in about 20 minutes! Check out how it works: https://youtu.be/_kiP6q8DX5c The agent was able to confirm exactly which option to select in EFTPS for my penalty payment and even verified my payment had been correctly applied after I submitted it while still on the call. Saved me so much stress wondering if I did it right. Before using Claimyr, I spent three separate days trying to get through on my own with no luck.

0 coins

GalacticGladiator

•8M

The service basically keeps dialing for you using their system and then calls you once they reach an agent. It works by navigating the IRS phone tree automatically, then waiting on hold so you don't have to. When an agent picks up, you get a call connecting you directly. To address the skepticism - I completely understand because I felt the same way initially. But it's not about doing something you can't do yourself; it's about saving hours of your time. I had already spent over 8 hours across multiple days trying to get through. With Claimyr, I was able to go about my day and only got on the phone when an actual agent was ready to talk. It's basically like having someone else wait in line for you.

0 coins

Aisha Hussain

•8M

I need to apologize for my skepticism earlier. After another failed attempt to reach the IRS yesterday (2 hours on hold before being disconnected), I broke down and tried Claimyr. I got a call back in about 35 minutes with an actual IRS representative on the line! The agent walked me through exactly how to pay my LLC's late filing penalty on EFTPS. They confirmed that "Balance due on return or notice" was correct, and explained that the warning about the tax period being out of range is normal for older penalties. They even gave me a confirmation number I could reference if there were any issues with how the payment was applied. So yeah... I was wrong and it actually worked. Saved me a ton of frustration.

0 coins

Yuki Yamamoto

•8M

Just thought I'd add that I had success using the "Balance due on return or notice" option on EFTPS for my partnership's late filing penalty. After selecting that and entering the tax year, I ignored the warning about the unusual tax period and continued. Make sure you print the confirmation page after completing the payment! I didn't do this initially and had a minor panic attack later when I couldn't remember if I'd completed all the steps. Ended up having to call the IRS to confirm the payment went through (took forever to reach someone).

0 coins

Yuki Yamamoto

•8M

I entered "1065 Late Filing Penalty" followed by the tax year in the reference field. The IRS agent I eventually spoke with said this was perfect because it clearly identified what the payment was for. If you have a CP notice or letter number from the IRS, definitely include that too (mine was CP541). The most important thing is that you're using the same EIN on EFTPS that's associated with your 1065 filing. That's how the system ultimately links your payment to the right account. The reference field just makes it easier for them to apply it correctly if there's any confusion.

0 coins

Zoe Dimitriou

•8M

Yes! I got a full abatement on a $1,450 late filing penalty for my LLC last year. Write a letter requesting "first-time penalty abatement" if you've had clean compliance for the past 3 years. Include your EIN, the penalty amount, tax year, and an explanation. Emphasize your good filing history. Send it certified mail to the address on your notice. Mine was approved in about 6 weeks. Even if you've already paid (like I did), they'll refund the penalty amount if approved. Don't forget to specifically use the phrase "first-time penalty abatement" in your letter - that's the official program name!

0 coins

CosmicCommander

•5M

I just went through this exact same process last month for my LLC's late filing penalty! You're definitely on the right track with selecting "Balance due on return or notice" - that's the correct option for penalty payments. The warning message about the tax period being out of the usual range is completely normal when you're paying an older penalty. Don't let it scare you - just click "Continue" and proceed with the payment. The system shows this warning for any tax year that's not the current or immediately previous year. A few tips from my experience: - Make sure you're logged into EFTPS with your LLC's EIN, not your personal SSN - In the reference field, enter something like "Form 1065 Late Filing Penalty 2019" to make it crystal clear what the payment is for - Print or save the confirmation page - you'll want that reference number - The payment typically processes within 1-2 business days The $2,600 amount sounds about right for a multi-year late filing penalty. Once you submit the payment, you can check your account transcript online in about a week to confirm it was applied correctly to your penalty balance.

0 coins