How Long Does a CIS Tax Refund Take? (2026/27 Timelines)

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 honest answer: HMRC does not publish one

Search this question and you will be given a number. Five working days, ten working days, two to four weeks, eight to twelve weeks. None of them comes from HMRC, because for a Self Assessment repayment HMRC does not publish a processing time at all.

What it publishes instead is a tool. "Check when you can expect a reply from HMRC" on GOV.UK lists, service by service, the date HMRC is currently working to, and it is updated weekly. There is a separate line for Self Assessment repayment claims, and separate lines for online and paper work. The date it shows in April is not the date it shows in February, which is precisely why a fixed figure published in an article cannot be right for long.

That is the number to go and get. It takes under a minute, it is specific to the service you are waiting on, and it is the only figure on this subject that is both sourced and current.

One figure does get quoted with a source attached. HMRC has told ICAEW that where a repayment is selected for its security checks, those checks can take up to a further 12 weeks. The word doing the work there is further: 12 weeks on top of the date the tool gives you, not a total from filing. Treat it as the tail risk on the timeline rather than the timeline itself.

You will also see a 5 working day figure quoted on GOV.UK. It is real, but it belongs to a different thing entirely: claiming a PAYE tax refund online after a P800 calculation, where the 5 days covers the payment reaching your account once you have claimed. It is not a Self Assessment timescale and it does not apply to a CIS subcontractor filing a return.

What the pipeline actually consists of

Durations are not publishable, but the sequence is, and knowing it tells you which stage you are sitting in when nothing appears to be happening.

Stage	What happens	What governs the timing
1. Tax year ends	You cannot file for 2026/27 until 6 April 2027	Fixed in law. Nothing moves before this date
2. Return filed	You (or your accountant) submit the return online	Entirely within your control, and the only stage that is
3. HMRC processing	HMRC reconciles the return against the CIS deductions contractors have reported and calculates the repayment	No published time. Check the current date on HMRC's reply-times tool
4. Security check, if triggered	HMRC pauses the repayment and writes to you for evidence	Up to a further 12 weeks (HMRC, via ICAEW). Your response time is part of it
5. Repayment issued	HMRC pays the bank account held on your Government Gateway, or posts a cheque if none is held	Add bank clearing. A missing bank detail turns a transfer into a cheque

Two practical conclusions follow. Stage 2 is the only lever you hold, and stage 4 is the only delay anyone has quantified. Everything worth doing about this timeline is aimed at one or the other.

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.

The arithmetic of filing early does not depend on knowing HMRC's processing time, which is what makes it the reliable advice. A deduction suffered in May 2026 falls in the 2026/27 tax year. File on 10 April 2027, the week the year closes, and the claim is with HMRC that week. File on 28 January 2028, the legal deadline, and the same claim starts more than nine months later. Whatever HMRC's queue is doing, those nine months are added by you, not by them.

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 reports them on its monthly Employer Payment Summary and pays HMRC a reduced PAYE and National Insurance bill. The important point about the timing is the one most guides miss: the company is not waiting on HMRC at all. It is not a claim, it is an offset the company applies to its own payment, so there is no queue, no processing and no turnaround. If the CIS suffered exceeds the PAYE liability in a month, the surplus carries forward and reduces the next month's bill.

Only what is left over after the tax year ends becomes a repayment claim HMRC has to process, and that one does have a published figure: GOV.UK says HMRC will usually respond within 8 weeks of a limited-company CIS repayment claim. Note that this is a response, not necessarily the money.

Set that against the sole-trader position. A deduction taken early in the tax year is not recoverable until that year's return is filed after the following 5 April, so depending on when the deduction fell and when the return goes in, the gap between losing the cash and getting it back can run from several months to around 22 months. The limited-company advantage is structural, and it does not depend on HMRC being quick.

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.

Before you chase, check the current date on HMRC's "Check when you can expect a reply from HMRC" tool. A repayment is not late until that date has passed, and the helpline will tell you the same thing. Once it has passed 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.