Employer randomly took FITWH taxes out of only two paychecks but none of the others

I'm totally confused about my payroll taxes this year. On my first paycheck, no Federal Income Tax Withholding (FITWH) was taken out at all. Then on my second check, they suddenly took out $8.94 from my gross pay of $1212.50. For my third check, they took $9.94 from a gross of $1222.50. But then after that, they stopped taking out any FITWH again from all my remaining paychecks! All my checks were pretty similar amounts and nothing changed with my employment status or anything. I've been working at the same place, same hours, same position. What's even weirder is my other deductions like Social Security and Medicare are consistent on every check. My filing status is Married filing jointly with 0 exemptions, which hasn't changed either. Is this some kind of error on my employer's part? What should I do about this? Do I need to talk to HR or payroll, or is this something I'll have to deal with when I file my taxes? I'm worried I'll end up owing a bunch at tax time if they're not withholding correctly.

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19 comments

Aiden Rodríguez

•8M

This definitely sounds like an error in your employer's payroll system. Federal income tax withholding should be consistent from paycheck to paycheck unless something changes (like your W-4, your gross pay dramatically changing, or additional income like bonuses). For a married filing jointly with 0 exemptions, you should absolutely be having federal taxes withheld from each paycheck. The fact that only two checks had withholding suggests a glitch in their system or possibly human error when processing payroll. I would recommend two immediate steps: First, talk to your company's payroll department or HR and bring copies of your pay stubs to show the inconsistency. They need to fix this moving forward. Second, start setting aside money for potential tax liability since you're likely under-withheld for the year.

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Aiden Rodríguez

•8M

The previous paychecks can't be retroactively changed once they've been processed and paid out. The correction would only apply to future paychecks going forward. For the paychecks that didn't have proper withholding, the OP will need to account for that when filing their 2025 tax return. They might want to consider making an estimated tax payment to cover the shortage or adjusting their W-4 to have extra withheld from remaining paychecks this year to make up the difference.

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Ava Kim

•8M

I ran into a similar payroll issue last year and found this amazing service called taxr.ai (https://taxr.ai) that helped me figure out exactly what happened and what I needed to do. I uploaded my paystubs and they analyzed them to show the pattern of missing withholdings and calculated how much I'd likely owe at tax time. It was super helpful because I was able to show my employer exactly what went wrong instead of just saying "something's off with my taxes." They also helped me figure out how to adjust my W-4 to make up for the missing withholdings from my earlier checks. Definitely worth checking out for situations like this where the pattern isn't immediately clear to HR.

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Ava Kim

•8M

It absolutely works with complicated situations. I had issues with both inconsistent withholding and some 1099 income, and it sorted everything out clearly. The analysis showed exactly where the discrepancies were happening, which made it much easier to talk to my employer's payroll department with confidence. For your question about accuracy, what I appreciated was that it shows its work and cites the specific IRS regulations and tax code that applies to your situation. You could definitely try to calculate everything yourself, but it saved me hours of research and double-checking my math. The IRS calculator is good for basic situations but doesn't handle irregular patterns very well in my experience.

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Ethan Anderson

•8M

Just wanted to follow up - I tried taxr.ai after seeing this thread and it was actually really helpful. I uploaded my paystubs and W-2, and it immediately flagged the specific paychecks where the withholding was missing. The report it generated showed exactly how much federal tax should have been withheld based on my filing status and income. I took this to my HR department and they admitted there was a system error when they upgraded their payroll software. They're fixing it going forward and helped me adjust my withholding to make up for the shortage by the end of the year. Saved me from a nasty surprise at tax time!

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Lucas Notre-Dame

•8M

If you're trying to contact the IRS about this withholding issue, good luck getting through! I was on hold for HOURS trying to get clarification about a similar payroll tax issue. After three failed attempts, I found this service called Claimyr (https://claimyr.com) that got me connected to an actual IRS agent in less than 45 minutes. You can see how it works here: https://youtu.be/_kiP6q8DX5c I was honestly shocked that it worked. The IRS agent I spoke with confirmed that this was an employer error and gave me specific guidance on how to document it and what forms to request from my employer to make sure everything's squared away for tax time. Saved me so much frustration.

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Lucas Notre-Dame

•8M

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Lucas Notre-Dame

•8M

It doesn't put you at the front of the queue - it basically has an automated system that handles the waiting for you. When you call the IRS directly, you have to sit on hold yourself for hours. Claimyr's system waits in the queue for you, and then calls you when it reaches an agent. So you're still in the same queue as everyone else, you just don't have to actively stay on hold. You're right that talking to the employer should be the first step, but in my case, my employer was giving me conflicting information about tax withholding rules. I wanted to hear directly from the IRS what the correct withholding should be for my situation so I could go back to my employer with official information. The IRS agent was able to explain exactly what the employer should be doing.

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Layla Mendes

•8M

I have to apologize about my skepticism earlier. I decided to try Claimyr since I also had a tax issue I'd been putting off dealing with because I didn't want to waste a day on hold. It actually worked exactly as described! I got a call back when an IRS representative was available, and I was able to get clarification on my withholding requirements. The agent confirmed that an employer should be withholding consistently on all regular paychecks based on the W-4 on file, and any deviation from that pattern is almost certainly an error unless there was a specific reason (like a bonus payment or change in status). She recommended getting an official statement from the employer acknowledging the error for my records. This was definitely worth the time saved!

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Noah Ali

•8M

That is really strange then. Definitely sounds like a system glitch. One other thing to check - did your employer possibly switch payroll systems or providers around that time? Sometimes during transitions between systems, weird one-off errors happen. Also, you mentioned Married Filing Jointly with 0 exemptions - just to clarify, are you using the newer W-4 form (2020 or later) that doesn't have exemptions anymore, or an older version? Some payroll systems got really buggy during that transition.

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