Why most subcontractors are owed a refund
Under CIS, a contractor deducts money from a subcontractor's payment as an advance against their tax and National Insurance. For 2026/27 the rate for a registered subcontractor is 20%, applied to the labour element only. On a £1,000 invoice split as £600 labour and £400 materials, the deduction is £120, not £200.
That 20% is taken before any expenses or personal allowance are counted. A sole trader who earns £45,000 in CIS income, claims £15,000 in expenses and has a £12,570 personal allowance owes tax on roughly £17,430, but 20% will have been deducted on the labour throughout the year. Most registered subcontractors overpay, and the overpayment is the refund.
If you want the full mechanics of how to make the claim, our guide to how to claim a CIS tax refund covers the step-by-step process. This article focuses on the timing: what the pipeline looks like, what can delay it and what you can do about each stage.
The Self Assessment to bank-credit pipeline
For a sole-trader subcontractor, every CIS refund runs through the same sequence. The table below maps each stage, the party responsible and the typical duration in normal conditions (no security check, online filing, no errors in the return).
| Stage | Action | Typical duration |
|---|---|---|
| 1. Self Assessment filed | Subcontractor (or their accountant) submits the online return to HMRC | Same day; instant online confirmation |
| 2. HMRC processing | HMRC reconciles the return against CIS deductions on record and calculates the repayment | 5 to 10 working days (HMRC online target) |
| 3. Security check (if triggered) | HMRC pauses the repayment and requests supporting evidence, typically by post | 4 to 8 weeks additional (or longer if evidence is queried) |
| 4. Repayment instruction issued | HMRC authorises the repayment and sends an instruction to the bank | 1 to 2 working days after processing completes |
| 5. Bank receipt | The refund arrives in the subcontractor's bank account | 1 to 3 working days for bank clearing |
In a clean case, stages 1 to 2 to 4 to 5 run in roughly 2 to 4 weeks from the date the return is filed. That is the realistic expectation for an experienced filer whose figures match HMRC's records, who files online and who does not trigger a security check. The variable to manage is stage 3: a security check is the single biggest source of delay, and it is not random.
What triggers an HMRC security check
HMRC runs automated checks on repayments before authorising them. Three categories of return are much more likely to be paused for review than others.
First-time filers. If this is the first Self Assessment return you have filed, HMRC has no prior repayment history for you. Establishing that the return is genuine takes longer when there is no track record to compare it against. Expect a higher probability of a check in year one, and be ready to provide evidence of your CIS deductions (your CIS payment and deduction statements, which your contractors are required to give you monthly).
Large refunds. A repayment of £5,000 or more is more likely to attract scrutiny than one of £800. The financial risk from a fraudulent large repayment is higher, so HMRC applies more rigour. Extra scrutiny on a large genuine refund is a standard risk-based filter, not a sign that something is wrong on your return.
Incomplete or inconsistent returns. Where income figures do not match the CIS deduction amounts HMRC holds on record, or where expenses appear out of line for the trade, a manual review is likely. This is the most avoidable trigger: a return prepared accurately and with complete information is far less likely to be flagged than one with gaps or figures that look anomalous.
If a security check is opened, HMRC will write to you (usually by post) requesting specific evidence. Respond on the day you receive the letter and provide exactly what is asked for. Every day of delay at that stage is a day added to the total wait.
The January rush: why timing your filing matters
The Self Assessment deadline is 31 January. The majority of subcontractors who file their own returns do so in the weeks immediately before that deadline. The consequence is that HMRC's processing queue is longest and slowest between January and March, because hundreds of thousands of returns arrive in a short window.
A subcontractor who files in April, May or June, as soon as the tax year closes and the figures are ready, faces a much shorter queue. The 5 to 10 working day target reflects that lighter-traffic period. A subcontractor who files on 28 January may find that the same HMRC processing window stretches materially because of the volume of competing returns, and the cumulative wait to bank credit can run to 6 to 8 weeks in a busy February.
Filing early is the single cheapest and most reliable way to accelerate your refund. There is no reason to wait, and the cost of waiting is measured in weeks.
The limited company route: skip the long wait with the EPS
A sole trader reclaims via Self Assessment after the tax year closes. A limited company subcontractor has a better option available during the year itself: the Employer Payment Summary (EPS).
Under the EPS route, a limited company that suffers CIS deductions offsets them in real time against its monthly PAYE tax and National Insurance liabilities. Instead of paying HMRC the full PAYE amount each month, the company reduces it by the CIS deductions it has suffered. If the CIS deductions exceed the PAYE liability in a given month, the excess is carried forward or, where the position is persistently in credit, the company applies for a formal repayment.
HMRC's target for processing EPS repayment applications is 25 working days. That is roughly five calendar weeks from the date of the claim, which is considerably faster than the wait a sole trader faces between suffering the deductions and receiving a Self Assessment refund. A deduction taken early in the tax year is not recoverable until that year's return is filed after 5 April the following year, so depending on when the deduction fell and when the return is filed the wait can run from several months to around 22 months in the worst case.
The EPS requires the company to run payroll and file monthly EPS submissions through payroll software before the 19th of each month. Our guide to CIS reclaims for limited companies covers the EPS mechanics in detail.
How to track and chase your refund
Once you have filed, the first place to check is your HMRC online account at www.gov.uk/personal-tax-account. Log in and navigate to the Self Assessment section. Once HMRC has processed the return and authorised a repayment, the status will update and you will see an expected payment date. Check this before calling the helpline, because the information there is usually more current than what the helpline can access.
If more than 10 working days have passed since your return was received and the status has not moved, or if you have received a letter requesting evidence and want to confirm receipt of your reply, call the HMRC Self Assessment helpline on 0300 200 3210, available Monday to Friday, 8am to 6pm. Have your National Insurance number and Unique Taxpayer Reference (UTR) ready before you call.
The helpline cannot speed up a security check in progress, but it can confirm that one has been raised and tell you what evidence is outstanding. Responding to any HMRC information request on the day you receive it is the fastest lever you have once a review is running.
The 4-year lookback window
If you have missed CIS refunds from prior years, you have time to reclaim them, but only up to a point. HMRC allows Self Assessment refund claims to go back 4 prior tax years. For 2026/27 that means you can still file for 2022/23, 2023/24, 2024/25 and 2025/26.
Years outside the 4-year window are closed permanently. Given that registered subcontractors receive an average refund of around £2,000 per year (this is illustrative and based on third-party reported figures, not a guarantee for any individual), four unfiled years represents a significant sum that cannot be recovered once the window passes. Each year requires its own return. If you have outstanding years, the time cost of filing them is far smaller than the refund you stand to lose by leaving them unfiled.
What to do now
If you are a sole trader who has had CIS deductions taken this year or in recent years, the action is straightforward: file your Self Assessment return as soon as the figures are ready after 5 April, do not wait until January, and make sure your CIS payment and deduction statements are in order before filing so the figures match what HMRC holds. If you have prior years outstanding, check how many are still within the 4-year window and file for each one separately.
If you operate through a limited company, check whether you are making full use of the EPS offset each month. If not, the gap between what you could be recovering in-year and what you are actually recovering may be substantial.
Our CIS refund estimator can give you a quick indication of what a refund might look like based on your CIS income and expenses, before you file. And if you would like a specialist to handle the filing, the CIS-to-Self-Assessment review and any correspondence with HMRC on your behalf, our CIS refund service is built around exactly this process. The refund is the starting point for an ongoing relationship, not a one-off transaction, and getting the first return right sets the foundation for everything that follows.