Even with the best payroll software, mistakes happen — a wrong tax code, a miscalculated overtime payment, an employee accidentally paid twice, or figures reported incorrectly to HMRC through Real Time Information. The good news is that HMRC has a well-established process for correcting payroll errors, and how you fix it depends mainly on when the mistake is discovered and whether it affected the employee’s pay, the figures reported to HMRC, or both.
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Step 1: Identify Exactly What Went Wrong
Before correcting anything, pin down the specific nature of the error:
- Pay or deduction error: the employee was paid the wrong gross amount, or Income Tax/National Insurance was calculated incorrectly
- Reporting error: the employee was paid correctly, but the Full Payment Submission (FPS) sent to HMRC contained the wrong figures
- Payment date error: the wrong payment date was recorded, misaligned the payment with the incorrect tax period
- Employee information error: incorrect start or leaving dates, National Insurance category, or personal details
Compare the current period’s figures against year-to-date totals in your payroll software or submission log to confirm exactly where the discrepancy lies before making any correction.
Correcting the Figures Reported to HMRC
You cannot “reverse out” an FPS once it’s been submitted — instead, corrections are made by reporting the correct year-to-date figures going forward:
- If discovered within the same tax year: simply include the corrected year-to-date figures in your next regular FPS. There’s no need to resubmit each individual period separately; the correction flows through as an adjustment to the running total.
- If discovered shortly after the tax year ends (broadly, up to 19 April): you can generally still submit an additional FPS with corrected year-to-date figures as at 5 April for the previous tax year.
- If discovered later, after the final submission deadline has passed: a correction for an earlier tax year is generally still possible, but the process depends on your payroll software and how far back the correction relates — this is worth checking with your payroll provider or accountant, since the mechanism has changed in recent years and older correction methods (such as the Earlier Year Update) are being phased out for more recent tax years.
Correcting a payment date specifically follows a slightly different approach — an additional FPS with the correct payment date, marked with the appropriate late reporting reason, is generally the right route.
Will You Be Penalised for a Payroll Error?
Not automatically. HMRC has confirmed that a penalty only applies where the employer failed to take reasonable care or acted deliberately — a genuine, promptly corrected mistake generally doesn’t attract a penalty on its own. This is a similar principle to the behaviour-based penalty framework used elsewhere in the tax system, and it’s another reason to correct errors as soon as they’re identified rather than leaving them unaddressed.
If You Underpaid an Employee
Once the correct figures are established, the shortfall generally needs to be paid to the employee as soon as practicable, alongside the corrected PAYE reporting. Underpaying employees, even accidentally, can create separate employment law issues if it results in pay falling below the National Minimum or Living Wage for the hours worked, so it’s worth checking this specifically where an underpayment has occurred, not just correcting the PAYE figures.
If You Overpaid an Employee
Recovering an over-payment from an employee is more sensitive than it might first appear. While employers generally have the right to recover a genuine over-payment, doing so requires careful handling:
- Communicate clearly and promptly with the employee about the error and the proposed recovery
- Have a documented policy, or agree a reasonable repayment arrangement, particularly for larger amounts, rather than deducting the full sum from a single payslip without warning
- Be cautious about reducing a single deduction to the point where it takes pay below the National Minimum Wage for that pay period
- Keep clear records of the error, the amount, and how it was recovered, in case questions arise later
Unilaterally deducting a large over-payment without any communication can create genuine employment relations problems, even where the employer is technically entitled to recover the money.
Correcting Employer Payments to HMRC
A common misconception is that correcting an earlier period’s FPS changes what was owed to HMRC for that earlier period. In practice, corrections to previously reported figures typically adjust the payment due for the period in which the correction itself is submitted, not the original period — so if you correct a Month 3 error in Month 6, the adjustment generally shows up in your Month 6 liability to HMRC, rather than reopening the Month 3 payment.
What If HMRC’s Records Still Show the Wrong Figures?
If you’ve checked that the correct information was submitted via your RTI returns but HMRC’s own systems still show something different, this points to an error on HMRC’s end rather than in your submissions. In this situation, you can use HMRC’s dedicated service to query and correct an employer PAYE bill discrepancy, rather than resubmitting figures you’ve already confirmed are correct.
Preventing Payroll Errors Going Forward
A few habits significantly reduce the risk of recurring payroll errors:
- Reconciling payroll reports against bank payments each pay period, not just at year end
- Double-checking tax codes when HMRC issues updated notices, rather than assuming they’re correct
- Using payroll software that clearly flags year-to-date discrepancies before submission
- Reviewing new employee starter information carefully, since incorrect starter declarations are a common source of tax code errors
See our guide on small business payroll explained for a broader introduction to running payroll correctly from the outset.
How Felix Accountants Can Help
We help small employers correct payroll errors quickly and properly, handle the sensitive process of recovering over-payments from employees, and set up ongoing payroll processes that reduce the chance of errors recurring. Our payroll services can also take this off your hands entirely, running your payroll and managing HMRC reporting on your behalf.
Frequently Asked Questions
Can I fix a payroll error from an earlier pay period myself?
Yes, in most cases you correct it by including the updated year-to-date figures in your next regular FPS, rather than resubmitting the earlier period separately.
Will HMRC fine me for a genuine payroll mistake?
Not automatically. Penalties generally only apply where reasonable care wasn’t taken or the error was deliberate — a promptly corrected genuine mistake usually doesn’t attract a penalty.
Can I deduct an over-payment from an employee’s next payslip without telling them?
It’s strongly advisable not to. While employers generally have the right to recover a genuine over-payment, doing so without clear communication can create employment relations issues, and deductions shouldn’t reduce pay below the National Minimum Wage for that period.
Does correcting an old payroll error reopen what I owed HMRC for that earlier period?
Generally no. Corrections to earlier periods typically adjust the payment due for the period in which the correction is submitted, rather than reopening the original month or quarter’s liability.
What should I do if HMRC’s records don’t match what I submitted?
If you’ve confirmed the correct figures were submitted via RTI, this usually indicates an error on HMRC’s end, and you can use HMRC’s dedicated service to query and resolve the discrepancy.
Let’s get your payroll error corrected properly. Book your free 15-minute consultation with Felix Accountants.










