You've done the hard part. You filed your Self Assessment, claimed your CIS deductions, and HMRC owes you a refund. Now the question that every subcontractor asks: where is it?
The honest answer is that it depends — on when you filed, how you filed, and whether HMRC decides to look more closely at your return. This guide breaks down exactly what happens at each stage, what causes delays, and what you can do to push things along.
"HMRC doesn't have a fixed published turnaround time for CIS refunds. What it does have is a process — and once you understand that process, you know exactly where the bottlenecks are."
Not Sure How Much HMRC Owes You?
Before chasing a refund, make sure you know the correct amount. Our free calculator works it out in under 2 minutes — based on your actual CIS deductions and expenses.
CHECK YOUR REFUND NOW →✓ No registration required · 100% Free · HMRC 2026/27 Aligned
The Typical CIS Refund Timeline
Here's what the process looks like from the moment you click "submit" on your Self Assessment to the moment the money appears in your account.
0
You Submit Your Self Assessment Online
Your return is received by HMRC's systems immediately. You'll get an online confirmation. This is the start of the clock.
1–7
HMRC Processes Your Return
HMRC runs automated checks on your figures. Your CIS deduction claim is cross-referenced against what your contractors reported to HMRC each month. If the numbers match, you move forward quickly. If they don't, this is where a delay can start.
2–4
Repayment is Approved (Straightforward Cases)
For returns with no mismatches and no flags, HMRC approves the repayment within 2 to 4 weeks. You'll see a status update in your HMRC online account.
4–8
Payment Reaches Your Bank Account
Once approved, HMRC processes the bank transfer. This typically takes a further few days to a week. Most straightforward CIS refunds land within 4 to 8 weeks of submission.
8–12+
If a Compliance Check is Triggered
If HMRC selects your return for a compliance check — which can happen for any return, not just ones with errors — the timeline resets. These checks typically take 8 to 12 weeks from the date of the check letter, sometimes longer.
What HMRC Actually Does With Your CIS Figures
Understanding this step is the key to understanding why timelines vary. When you claim CIS deductions on your Self Assessment, you're telling HMRC: "My contractors deducted X from my payments this year."
HMRC then checks this against a separate set of records: the monthly CIS returns that your contractors submitted throughout the year. These returns list every subcontractor they paid, the amount, and the deduction taken. If your figure matches their records, the process is smooth. If it doesn't — even by a small amount — HMRC flags the discrepancy.
Not sure what your CIS statements should show? Read our full guide to CIS payment and deduction statements — what every figure means and why keeping them is essential before you file.
The Most Common Source of Delays: Mismatched Figures
The single most common reason a CIS refund is delayed isn't a mistake on your return — it's a mismatch between your claim and what your contractor reported. This happens more often than you'd think:
- A contractor submitted their monthly return late or used the wrong figures
- You worked for a contractor who didn't register properly for CIS
- A payment was included under a different UTR number by mistake
- Materials were incorrectly included in the deduction calculation
If any of these apply, HMRC will pause your refund until they've verified the numbers. You may receive a letter asking for further information, or the return may simply sit in a queue with no communication.
Early vs Late Filing: What the Numbers Show
The timing of your submission has a significant effect on how quickly you receive your refund. Here's how two subcontractors with identical claims can experience very different timelines.
| Filed | May 2026 |
| HMRC volume | Low — quick processing |
| Refund approved | ~3 weeks |
| Money in account | ~5 weeks total |
| Filed | January 2027 |
| HMRC volume | Peak — highest of the year |
| Refund approved | ~6–8 weeks |
| Money in account | ~10–12 weeks total |
The tax year ends 5 April. You can file your Self Assessment from 6 April onwards. Filing in April or May means you're ahead of 90% of other filers — and HMRC's workload is at its lowest.
How to Check Where Your Refund Is Right Now
You don't have to sit and wait. HMRC's online account gives you a real-time view of your Self Assessment status. Here's how to use it.
-
1
Log in to your HMRC online account Go to gov.uk and sign in with your Government Gateway user ID and password. If you've forgotten these, use the "problems signing in" link on the HMRC login page.
-
2
Navigate to Self Assessment Once logged in, select "Self Assessment" from your account dashboard. This shows your current tax position and any returns you've filed.
-
3
Check your return status Look for the status of your most recent return. If it shows "Repayment pending" or similar, your refund is in the queue. If it shows "Repayment sent," check the date — bank processing takes a few additional working days.
-
4
Confirm your bank details are correct HMRC pays refunds by bank transfer to the account listed on your Self Assessment return. If you've changed bank accounts since filing, you'll need to update these details directly — log in, go to your Self Assessment account, and update the repayment bank account.
-
5
If it's been more than 8 weeks with no update — call HMRC Use the Self Assessment helpline: 0300 200 3310 (Monday to Friday, 8am to 6pm). Have your UTR number ready. Ask specifically: "Has my repayment been approved and when was it issued?" This gives you a concrete answer rather than a general queue time.
If HMRC Has Written to You About Your Return
Receiving a letter from HMRC about your Self Assessment does not automatically mean something is wrong. HMRC routinely selects returns for compliance checks — these are not always triggered by errors. However, a compliance check does pause your refund until the check is complete.
If you've received a letter:
- Read it carefully — HMRC will specify exactly what they're querying and what evidence they need
- Respond within the deadline given — typically 30 days from the date of the letter
- Gather your CIS payment and deduction statements — these are your primary evidence
- Keep records of all expenses you've claimed — receipts, invoices, and mileage logs
Responding promptly and with complete documentation typically resolves compliance checks in 4 to 8 weeks. Ignoring the letter extends this significantly and can result in HMRC amending your return — which may reduce or eliminate your refund.
Claiming the right expenses is what makes the difference between a small refund and a meaningful one. Read our complete guide to CIS subcontractor expenses — every allowable cost and how to document it correctly.
How Far Back Can You Claim? The 4-Year Rule
If you've worked under CIS for multiple years and never filed a Self Assessment — or filed but didn't claim all your deductions — there may be more money owed to you than just this year's refund.
HMRC allows you to claim CIS refunds for up to 4 tax years. After this window closes, the right to claim expires permanently and HMRC keeps the money.
| 2025/26 | ✓ File now (deadline 31 Jan 2027) |
| 2024/25 | ✓ Still claimable |
| 2023/24 | ✓ Still claimable |
| 2022/23 | ✓ Still claimable |
| 2021/22 | ✗ Expired April 2026 — gone |
| Annual CIS deductions | £3,200/year |
| Actual tax owed | £1,400/year |
| Annual overpayment | £1,800/year |
| 3 years unclaimed | £5,400 total |
Each prior year requires a separate Self Assessment return. The process is the same — the timeline is the same — but multiply the paperwork by the number of years. HMRC processes prior-year returns in the same way as current-year ones.
The Refund Checklist: Before You Chase HMRC
Before calling HMRC's helpline, work through this list. Most refund delays can be traced to one of these points — and several can be resolved without a call.
- I filed my Self Assessment online (not on paper)
- My bank details in my HMRC online account are correct and current
- My CIS deduction figure matches my payment and deduction statements
- I haven't received any letters from HMRC requiring a response
- It has been at least 4 weeks since I submitted (most refunds arrive within 8)
- I filed before January (if yes, expect a longer wait)
- My UTR number is correct on the return
- I have a Government Gateway login and can check my status online
Case Studies: Real Timelines, Different Outcomes
Straightforward claim, filed early — refund in 5 weeks
A groundworker in the East Midlands filed his 2025/26 Self Assessment on 20 April 2026, two weeks after the tax year ended. He had three contractors, all of whom had submitted correct monthly CIS returns. His CIS deduction claim of £4,100 matched HMRC's records exactly.
HMRC processed the return within 3 weeks and the payment of £2,340 arrived in his account on 25 May 2026. No letters, no calls, no delays.
✓ Total time: 35 days. The early filing window made the difference.
Late filing, compliance check — refund took 14 weeks
A plasterer in South Yorkshire filed on 28 January 2026 — three days before the deadline. His return included a CIS deduction of £5,600, but one of his contractors had submitted their monthly return late, creating a £900 discrepancy between his claim and HMRC's records.
HMRC sent a compliance check letter in early March 2026. He responded with his payment statements within two weeks. HMRC confirmed the figures, approved the refund, and payment arrived in mid-April 2026.
⚠ Total time: 14 weeks. Late filing + peak volume + one mismatch added 9 weeks to the timeline.
Frequently Asked Questions
How long does a CIS tax refund take from HMRC?
Most CIS refunds filed online via Self Assessment take 4 to 8 weeks to process. However, if HMRC selects your return for a compliance check, this can extend to 12 weeks or longer. Filing early in the tax year — between April and June — typically results in faster processing.
How will HMRC pay my CIS refund?
HMRC pays CIS refunds directly into the UK bank account you provided in your Self Assessment return. They do not issue cheques as standard. If no bank account is on file, you will need to contact HMRC to arrange payment.
Why is my CIS refund taking so long?
The most common reasons for delays are: HMRC selecting your return for a compliance check, missing or mismatched CIS deduction figures, a missing or incorrect bank account on your HMRC record, or high submission volumes during January and February peak season.
Can I check the status of my CIS refund?
Yes. Log in to your HMRC online account (Government Gateway) and navigate to Self Assessment. You can see whether your return has been processed and whether a repayment has been issued. If it has been more than 8 weeks and no update is showing, you can call the Self Assessment helpline on 0300 200 3310.
How far back can I claim a CIS tax refund?
You can claim CIS refunds for up to 4 tax years. After 4 years, the right to claim expires permanently and HMRC keeps the overpayment.
Does filing a paper Self Assessment delay my CIS refund?
Yes, significantly. Paper returns must be submitted by 31 October and take longer to process than online returns. Filing online is always the recommended route for CIS subcontractors — it's faster to process and faster to pay.
Ready to claim your CIS refund?
Use our free calculator to find out what HMRC owes you — before you even pick up the phone.
CHECK YOUR REFUND NOW →Need professional invoices fast?
Create clean, compliant CIS invoices in seconds with our free tool.
TRY FREE INVOICE GENERATOR →