CIS Tax · Refunds · 2025/26 Tax Year
You filed, the refund shows on your account, and nothing arrives. Most delayed CIS refunds come down to five causes. Each one has a fix, and some of them you can prevent before you file.
By QuoteDone Editorial Team · Last updated: 2 October 2026 · Checked against GOV.UK guidance
Your CIS refund is the 20% your contractors deducted, minus the tax you actually owe for the year. Once your return is filed, HMRC works out that figure and, if everything checks out, pays it to your bank.
"If everything checks out" is where refunds stall. This guide explains what "pending" really means, the five reasons HMRC holds or cuts a CIS refund, a worked example of the most expensive one, and the order to chase it in.
What "Pending" on Your HMRC Account Actually Means
GOV.UK is clear: a refund showing as pending has been created but still needs to be approved and paid. It is not a refusal. It means HMRC has calculated the repayment and has not yet released it, usually because it is still being checked.
| What you see | What it means | What to do |
|---|---|---|
| Return filed, no refund shown yet | The return may still be processing. | Wait a few working days, then check again. |
| Refund "pending" | Created, not yet approved and paid. | Allow up to 4 weeks, then check Where's my reply. |
| Refund smaller than your calculation | Part may have been set against tax due, or CIS credited differently. | Compare your statement with your return (see cause 3 and 2 below). |
| Letter asking for information | A check is under way. | Reply by the deadline in the letter. |
HMRC does not publish a fixed timescale for Self Assessment refunds. Its guidance to tax agents says repayments are normally issued within 2 weeks, with up to 4 weeks allowed before contacting HMRC. For live waiting times, use HMRC's Where's my reply tool. Source: GOV.UK – Claiming a tax refund.
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The 5 Reasons HMRC Holds or Cuts a CIS Refund
1. A pre-payment security check
HMRC screens repayments for fraud before releasing them. It does not publish what triggers a check, so there is no way to guarantee you avoid one. Where a repayment is selected for a security check, HMRC's Where's my reply tool has asked people to allow up to a further 12 weeks before contacting it.
Fix: make sure your personal details, address and bank details in your HMRC account are current, and reply quickly to any request. There is nothing else to "do" during a routine check except wait for the expected date and then chase.
2. Your CIS figures do not match your contractors'
HMRC checks the CIS deductions you claim against the monthly returns your contractors file. If a contractor filed late, reported different figures, or reported you under the wrong details, your claim will not match HMRC's records. HMRC may then hold the refund, or credit only what it can see, and ask you for evidence.
Fix: before you file, total every monthly payment and deduction statement and compare it with the CIS figures in your HMRC online account. Chase any contractor whose statements are missing.
3. Tax you owe is taken from the refund
GOV.UK says you may not get a refund if you have tax due in the next 45 days, for example a payment on account. Instead, the money is deducted from the tax you owe. HMRC can also set a repayment against other amounts you owe it, including penalties.
Fix: check your Self Assessment statement for upcoming payments on account or outstanding charges. If the refund was reduced, the statement shows where the money went.
4. Missing or out-of-date bank details
If the bank details HMRC holds for the repayment are missing or wrong, the money cannot go straight to you. Check the repayment details on your return and in your HMRC online account before filing, especially if you have changed banks.
5. An error on the return itself
The refund is calculated from what you enter. If your CIS deductions are in the wrong place, or income and deductions do not add up, the calculation is wrong from the start. On the short self-employment pages (SA103S), CIS deductions go in Box 38. On the full pages (SA103F), they go in Box 82.
Fix: if you spot an error, you can correct your return online. GOV.UK explains how in If you need to change your return.
Worked Example: One Missing Contractor Statement
Figures use the 2025/26 rates: Personal Allowance £12,570, Income Tax 20%, Class 4 NIC 6%.
£40,000 labour, £6,200 expenses, one contractor's deductions not on HMRC's record
Nearly half the refund (£1,200 of £2,480.20) depends on one contractor's paperwork. That £1,200 is recoverable, but only once you prove it with payment and deduction statements and bank records.
File Early, Get Paid Early
A security check or mismatch adds weeks. Filing late adds months before the clock even starts. The same £2,480.20 refund, filed at two different times, allowing 4 weeks each time:
| Filed 20 May 2026 | Filed 20 January 2027 | |
|---|---|---|
| 4 weeks later | 17 June 2026 | 17 February 2027 |
| Time to fix a mismatch before the deadline | Over 8 months | 11 days |
| Risk of a late filing penalty if something goes wrong | Low | High: £100 from 1 February 2027 |
Refund Delayed? Chase It in This Order
- Check your HMRC online account. Look at your Self Assessment statement: is the refund pending, paid, or reduced by a set-off?
- Check Where's my reply. If HMRC is still within its expected date for your type of claim, calling will not speed it up.
- Match your CIS figures. Compare your statements with the CIS figures in your account. If one is missing, contact that contractor and keep the evidence ready.
- Contact HMRC once the date has passed. Call the Self Assessment helpline on 0300 200 3310 or use HMRC webchat, with your UTR ready. For questions about contractor records, the CIS helpline is 0300 200 3210.
- Answer every letter by its deadline. Send what is asked for, keep copies, and note the date you replied.
- Complain if the delay is unreasonable. HMRC has a formal complaints process on GOV.UK.
Before You File: The Delay-Proof Checklist
- Every monthly payment and deduction statement for 6 April 2025 to 5 April 2026 collected
- Total CIS on your statements matches the CIS figures in your HMRC online account
- CIS deductions entered in Box 38 (SA103S) or Box 82 (SA103F)
- Bank details for the repayment current and correct
- Address and contact details up to date in your HMRC account
- Receipts and mileage log saved, and kept at least 5 years after the 31 January deadline
Frequently Asked Questions
Why is my CIS refund delayed?
The most common reasons are a pre-payment security check, a mismatch between the CIS deductions on your return and what your contractors reported to HMRC, tax you owe being set against the refund, and missing or out-of-date bank details. An error in the CIS deductions box on your return can also stop the refund being calculated correctly.
How long does a CIS refund take?
HMRC does not publish a fixed timescale. Its guidance to tax agents says Self Assessment repayments are normally issued within 2 weeks and asks you to allow up to 4 weeks before contacting HMRC. Returns selected for security checks take longer: HMRC has asked people to allow up to a further 12 weeks in those cases. For current waiting times, use the Where's my reply tool on GOV.UK.
What does pending mean on my HMRC account?
GOV.UK says a pending refund has been created but still needs to be approved and paid. It usually means HMRC is still checking the claim. It does not mean the refund has been refused.
Why is my CIS refund less than I expected?
HMRC may have used part of it to cover tax you owe. GOV.UK says you may not get a refund if you have tax due in the next 45 days, for example a payment on account; instead the money is deducted from the tax you owe. HMRC may also have credited less CIS than you claimed if a contractor's figures do not match yours.
What happens if my contractor did not report my CIS deductions?
HMRC checks the CIS deductions you claim against the monthly returns your contractors file. If a contractor's figures are missing or different, HMRC may hold or reduce the refund and ask you for evidence. Send copies of your payment and deduction statements, and bank records showing the net payments you received.
Does HMRC contact you by email or text about a tax refund?
No. HMRC does not tell you about a tax refund by email or text, and does not ask for bank details that way. Forward suspicious emails to phishing@hmrc.gov.uk and texts to 60599, then delete them.
How do I chase a delayed CIS refund?
First check the status in your HMRC online account and the Where's my reply tool. If the expected date has passed, call the Self Assessment helpline on 0300 200 3310 or use HMRC's webchat, with your UTR ready. If HMRC has asked for information, reply by the deadline in its letter. If the delay is unreasonable, you can make a formal complaint to HMRC.
Important: This article is general information about HMRC processes for the 2025/26 tax year, not personal tax advice. HMRC's processing times and checks vary case by case. Always verify against GOV.UK or speak to a qualified accountant.
Author: QuoteDone Editorial Team · Published: 29 March 2026 · Last updated: 2 October 2026
Sources: GOV.UK – Claiming a tax refund · GOV.UK – Where's my reply · GOV.UK – Changing your return · GOV.UK – Complain to HMRC · GOV.UK – Business records
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