If contractors have taken CIS deductions from your pay this year, you're probably wondering two things: when you can get any overpayment back, and how long HMRC takes to pay it. This guide covers both for sole traders and partners, using GOV.UK's own timescales. Limited companies work differently, and there's a short section on them near the end.
The short answer
- When: after the tax year ends on 5 April. GOV.UK says the deductions are "advance payments towards your tax", and they're settled through your Self Assessment return for that year. You can send the return any time after 5 April. For the 2025–26 tax year, that's any time from 6 April 2026 until the online deadline of 31 January 2027.
- How long: if you're due a refund, GOV.UK says you'll usually get it within 2 weeks of sending your return online.
- If it's slow: GOV.UK says security measures "may cause a delay of up to 12 more weeks". Contact HMRC if you haven't been paid after 14 weeks in total.
Not everyone gets money back. GOV.UK says HMRC "will work out how much tax you owe and take off any deductions taken by contractors". If you still owe tax after that, it's due by 31 January. If the deductions come to more than you owe, "HMRC will pay the money back".
Step 1: The tax year has to end first
A sole trader's CIS deductions are settled once, for the whole tax year (6 April to 5 April). GOV.UK's pay tax and claim back deductions page says: "At the end of the tax year, send in your Self Assessment tax return as usual."
There's one exception during the year. If you stop trading, GOV.UK says "You may be able to get a refund of deductions you've already paid this tax year", using form CIS40 (sole traders) or CIS41 (partners).
Step 2: Wait for your last statement
The last tax month of the year ends on 5 April. GOV.UK's get paid page says contractors must give you each statement "within 14 days of the end of each tax month". So the final statement for the year should reach you by 19 April.
That statement matters. The return asks for your total pay before deductions and your total CIS deductions for the year. If a month is missing, so is part of your total.
Step 3: Send the return
GOV.UK's sending a return page lists what sending it earlier gets you. You:
- find out what you owe
- can budget, if you want to make weekly or monthly payments
- have time to pay your bill by 31 January
- can set up a payment plan, if you don't think you can pay on time
For 2025–26, a paper return must reach HMRC by 11:59pm on 31 October 2026. The online deadline is 11:59pm on 31 January 2027.
Step 4: How the refund reaches you
GOV.UK's refund checker says to look at the section of your return headed "If you have paid too much tax":
- If you completed it, "you'll usually get a refund automatically". HMRC usually pays it to the account on your tax return. GOV.UK says HMRC "can only pay refunds into UK bank accounts", and if you've paid HMRC by card, "HMRC will always try to refund to that card first".
- If you didn't, you claim it through your online account. If you file Self Assessment online, GOV.UK says to sign in and "Choose 'Request a Repayment' and follow the instructions". It says you'll usually get the refund within 2 weeks of making that claim.
Worked example (made-up figures)
Dan is a sole trader, and every figure here is invented. His 2025–26 statements show £4,000 of CIS deductions in total. When he sends his return, HMRC's calculation puts his tax and National Insurance for the year at £3,000. He owes nothing else to HMRC. So the deductions are £1,000 more than his bill.
The dates depend on when he sends the return:
| Dan sends his return online on | Usually paid within 2 weeks, by | Contact HMRC if still unpaid after 14 weeks, from |
|---|---|---|
| 2 November 2026 | 16 November 2026 | 8 February 2027 |
| 30 January 2027 | 13 February 2027 | 8 May 2027 |
The rules are the same in both rows. The only difference is the date he sends the return. The middle column is the usual case, not a promise. The right-hand column is GOV.UK's point to get in touch.
What can reduce or hold up a refund
- Tax due soon. GOV.UK says you may not get a refund "if you have tax due in the next 45 days (for example for a payment on account)". Instead, the money is taken off what you owe.
- Security checks. These can add up to 12 weeks, as above.
- Asking twice. GOV.UK says: "If you got a submission reference, do not request the refund again. This could cause a delay."
- Questions about your deductions. GOV.UK says to keep your statements, "as HMRC might ask for evidence of your deductions when you pay tax and claim back deductions".
One more thing to watch: GOV.UK says "HMRC does not send details of tax refunds by email". Treat a refund email as suspicious.
Limited companies are different
A limited company doesn't use Self Assessment for this. GOV.UK tells companies to "Use your company's payroll scheme to pay tax with your deductions". If there are deductions left over after the end of the tax year, the company claims a refund separately. GOV.UK's limited company refund guidance says "You can claim for a tax year once it has ended", and "We'll usually respond to your claim within 8 weeks."
FAQ
My refund shows as "pending". What does that mean? GOV.UK says it "means that the refund has been created but still needs to be approved and paid".
Can I get my CIS back before 5 April? As a sole trader or partner, GOV.UK only describes a mid-year refund if you stop trading (forms CIS40 and CIS41). Otherwise, the deductions are settled through the return for the whole year.
Where can I check how long HMRC is taking? HMRC's check when you can expect a reply tool covers CIS and Self Assessment. GOV.UK says it's updated weekly.
I sent a paper return. When will I get it? GOV.UK says that for a paper return, you'll usually get a refund within 2 weeks of the date on your tax calculation letter (SA302).
Getting the totals right before you send
The return needs two figures from a year of statements: total pay before deductions, and total CIS deductions. cissplit reads your statements (PDFs or photos) and checks the deduction rate on each one. It flags gaps between a contractor's months, then totals the tax year, with every statement listed by contractor. Your first 3 statements are free, with no sign-up. It doesn't fill in or send your return, and you still check the figures against your statements.
This isn't tax advice. Check GOV.UK's CIS guidance for subcontractors or an accountant for your situation, and check the figures before you submit anything.