Late FPS submission: what HMRC charges and how to put it right

The Full Payment Submission (FPS) — the report of pay and deductions every employer sends to HM Revenue and Customs (HMRC) under Real Time Information (RTI) — is due on or before each payday. When one goes in late, or not at all, HMRC's response follows a defined structure: a monthly penalty scaled to the size of your scheme, softened by two concessions and an appeals route. This guide sets out the amounts, the concessions, and the practical steps to put a missed or wrong submission right.

The rule you missed: on or before payday

The FPS deadline is the payday itself — the contractual payment date reported on the submission, not the end of the month and not a fixed calendar date. An employer paying staff on the 25th must have the FPS with HMRC by the 25th; a weekly payroll generates a weekly deadline. If you are unsure what the FPS is or what goes in it, start with our guide to the Full Payment Submission; for how it fits into the wider reporting system, see what RTI is.

A submission counts as late when it arrives after the payday it reports — and a period with no submission at all counts as a failure for that month too.

The penalty amounts

Late-filing penalties are charged per tax month in which one or more filings were late, and the amount depends on how many employees are in the scheme:

Number of employees	Monthly penalty
1 – 9	£100
10 – 49	£200
50 – 249	£300
250 or more	£400

Two features of the design are worth noting. The penalty is per month, not per submission — a weekly payroll that files four FPS submissions late in one tax month faces one penalty for that month, not four. And where a scheme is more than three months late, HMRC can additionally charge a penalty of 5% of the tax and National Insurance that should have been reported — the escalation aimed at schemes that stop filing altogether rather than file late.

The one-late-submission-per-year concession

Your first late FPS in a tax year does not attract a penalty. This is automatic — no claim needed — and it resets each 6 April. It exists to absorb the genuinely occasional slip: a payroll run delayed by a bank holiday miscount, a submission that failed overnight. It does not accumulate; there is one free failure per tax year, not one per month or one per PAYE scheme size band.

The three-day easement

Separately from the annual concession, HMRC does not normally charge a penalty for an FPS that arrives within three days of the payday. The distinction matters: the deadline is still payday, and the three days are an easement HMRC applies when deciding whether to penalise, not extra filing time you are entitled to. HMRC has said plainly that employers who persistently file within the three-day window — treating it as a de facto extension — can be identified, reviewed and penalised. Use it as a safety net, not a schedule.

Late reporting reason codes

The FPS itself carries a field for a late reporting reason, used when a submission is unavoidably after payday. The codes cover recognised situations — for example a notional payment, a payment ad hoc or impractical to report on time, a reasonable excuse, or a correction to an earlier submission. Setting the right code when you file late does two things: it tells HMRC's automated systems why the submission is late before a penalty is raised, and it creates a contemporaneous record if you later need to appeal. Your payroll software should prompt for the code whenever the payment date on the FPS is in the past.

Appeals and reasonable excuse

If a penalty notice arrives, you can appeal — online through HMRC's service, or in writing — and the penalty is cancelled where you have a reasonable excuse for the failure. HMRC's benchmark is an unexpected or unusual event that prevented filing despite you taking reasonable care: serious illness, bereavement, fire or flood, or a failure of software or HMRC's own systems at the critical time. Predictable pressures — being busy, being short-staffed, not understanding the rules — do not usually qualify. Two practical points: file the outstanding FPS before or alongside the appeal (the excuse covers the delay, not an ongoing failure), and appeal promptly, as the notice carries a time limit.

It is also worth checking penalties rather than paying reflexively. If the notice covers your first failure of the year, or a submission that was within three days of payday, say so in the appeal — the concessions are grounds for cancellation.

How to correct a missed or wrong FPS

You missed the submission entirely

Send the FPS as soon as possible, with the payment date it should have carried and a late reporting reason code. Do not wait for the next pay run to fold it in — an unexplained gap is what triggers both penalties and estimated charges, and HMRC may raise a specimen charge for the missing period based on your filing history until real figures arrive.

The FPS went in on time but the figures were wrong

Correct the figures in your payroll software. Because HMRC works from year-to-date totals, the next regular FPS carries the corrected cumulative figures and overwrites the error — no resubmission of the faulty FPS is needed. If there is no later payday left in the tax year, or you find the error after 5 April, send an additional FPS showing the corrected year-to-date figures for the affected employees. This year-to-date FPS is also how closed years are amended, having replaced the old Earlier Year Update.

Nobody was paid — so there was no FPS to send

A month with no payments is not a late-filing problem, but silence still is. Send an Employer Payment Summary (EPS) reporting that no employees were paid in the period — our guide to the Employer Payment Summary covers when it is due and what else it does. Without it, HMRC assumes a return is missing rather than empty.

Preventing the next one

Almost every late FPS traces back to the same root cause: the submission is a separate step someone has to remember after running payroll. The fix is structural — use software where filing is part of the pay run itself, so approving payday and reporting to HMRC are the same action, and where a pay run that has not been submitted is visibly flagged before the date passes. Taxriva files the FPS to HMRC as each pay run is finalised, applies late reporting reason codes when a run is genuinely late, and keeps every acknowledgement as your evidence of on-time filing. See our FPS and EPS filing software page for how that works.

Quick reference

• FPS deadline: on or before payday, every pay run.
• Monthly penalties by scheme size: £100 / £200 / £300 / £400 (1–9 / 10–49 / 50–249 / 250+ employees).
• First late FPS of the tax year: no penalty. Resets each 6 April.
• Within three days of payday: not normally penalised — but persistent use is flagged.
• Filing late? Include a late reporting reason code on the FPS.
• Wrong figures: fix via year-to-date figures on the next FPS, or an additional YTD FPS after year end.
• Penalty notice unfair? Appeal — reasonable excuse, first-failure and three-day grounds all count.