Frequently Asked Question
What happens when you submit a payroll run late?
Last Updated 7 years ago
The following information is a summary of information provided by HMRC. To find out more about late reporting of payroll information, please visit the following link: https://www.gov.uk/guidance/what-happens-if-you-dont-report-payroll-information-on-time
- You didn't send the expected number of Full Payment Submissions.
- You didn't send an Employer Payment Summary when you didn't pay any employees in a tax month.
- You're a new employer and you sent your first Full Payment Submission within 30 days of paying an employee.
- It's your first failure to submit on time in the current tax year (this doesn't apply to employers who register with HMRC as an annual scheme).
If you're over 3 months late you can be charged an additional 5% of the tax and National Insurance that you should have reported.
If you run more than one PAYE scheme, you can be charged penalties for each.
You can appeal the charge if you think:
- The penalty is not due
- The amount of the penalty is wrong
- You had a reasonable excuse for sending your reports late
These are some of the reasons you can give as grounds for appeal:
- Data on the returns was incorrect
- Death/Bereavement
- Filing expectation incorrect
- Filed on time
- Fire/Flood/Natural Disaster
- Ill health
- IT difficulty
- Missed correction/easement
- No longer have any employees
- Theft/crime
- Other (if the appeal doesn't fall into any of the above categories)
When are penalties applied?
- The Full Payment Submission was late.- You didn't send the expected number of Full Payment Submissions.
- You didn't send an Employer Payment Summary when you didn't pay any employees in a tax month.
HMRC won't apply a penalty if:
- The Full Payment Submission is late but all reported payments on the submission are within 3 days of your employees' payday (applies from 6th March 2015 to 5th April 2018). Employers who persistently file after the payment date but within 3 days may still be considered for a penalty.- You're a new employer and you sent your first Full Payment Submission within 30 days of paying an employee.
- It's your first failure to submit on time in the current tax year (this doesn't apply to employers who register with HMRC as an annual scheme).
How much you pay
| Number of Employees | Monthly Penalty |
| 1 - 9 | £100 |
| 10 - 49 | £200 |
| 50 - 249 | £300 |
| 250+ | £400 |
If you run more than one PAYE scheme, you can be charged penalties for each.
Estimating what you owe
If you don't submit your Full Payment Submission on time or send an Employer Payment Summary, HMRC may raise a charge based on your previous PAYE payment and filing history. You can check any of these charges on your PAYE account online.If you get a penalty
Pay the penalty within 30 days of getting the notice - you'll be charged interest if you don't.You can appeal the charge if you think:
- The penalty is not due
- The amount of the penalty is wrong
- You had a reasonable excuse for sending your reports late
These are some of the reasons you can give as grounds for appeal:
- Data on the returns was incorrect
- Death/Bereavement
- Filing expectation incorrect
- Filed on time
- Fire/Flood/Natural Disaster
- Ill health
- IT difficulty
- Missed correction/easement
- No longer have any employees
- Theft/crime
- Other (if the appeal doesn't fall into any of the above categories)