Why is my CIS refund delayed?

Five things can hold up a CIS refund: security checks, deductions that do not match your contractors' returns, tax you still owe, bank details, and, under Making Tax Digital from April 2027, a refund never requested.

A refund under the Construction Industry Scheme (CIS) is the difference between the tax taken off your pay and the tax you actually owe for the year. HMRC pays it once it has checked your return against what your contractors told it. For normal timescales, see how long a CIS refund takes.

The usual causes at a glance

When your figures do not match

Every month, each contractor sends HMRC a return listing what it paid you and what it deducted. When you claim CIS deductions on your tax return, HMRC's CIS manual says an automated comparison is made between your claim and what your contractors reported. If the two do not match, HMRC may ask questions.

HMRC has two ways to change your claim. An officer can correct it within 9 months of your return being filed if information HMRC holds suggests it is wrong, and you then have 30 days to reject the correction. Or HMRC can open an enquiry into the return, which you can appeal against if you disagree with the result.

Take a self-employed bricklayer who claims £6,000 of deductions, but whose main contractor reported only £4,800. Until that £1,200 gap is explained, HMRC may restrict the refund to what it can confirm. The fix is a corrected return from the contractor, or the bricklayer's own statements and bank records.

When the contractor has not filed at all

HMRC's manual covers this case directly. Once the tax year has ended, credit is allowed for the deductions you claim on your Self Assessment return, unless a compliance officer opens an enquiry. In an enquiry, the officer may ask for bank statements to back up your payment and deduction statements, or invoices where you got no statements, and can limit the claim to what that evidence shows. If you are in that position, see what to do if your contractor has not paid your CIS deductions to HMRC.

When HMRC sets the refund against tax you owe

HMRC's manual says CIS deductions can be repaid only where they exceed both the tax and Class 4 National Insurance for the year and any of that tax still unpaid for another year. So a bricklayer owed £1,500 for 2025-26 who still owes £400 from 2024-25 may receive £1,100, with £400 set against the older bill. GOV.UK also says you may not get a refund if you have tax due in the next 45 days, such as a payment on account. HMRC takes it off that bill instead.

What this means for you

A delay is not always a problem with your claim. But a mismatch is the cause you can do most about, and the evidence is the same every time: your monthly statements and the bank entries that match them. If HMRC writes to you, reply by the date it gives.

Steps if your refund is late

1. Sign in to your HMRC online account and check whether the refund shows as pending, as credit or not at all.
2. Check your statement for tax owed from an earlier year, or a payment on account due soon.
3. Confirm the bank account on your return is a UK account and the details are right.
4. Add up your statements for 6 April to 5 April and compare them with the deductions you claimed.
5. If any contractor's figure looks wrong or missing, ask them to check their monthly return.
6. If you have not been paid 14 weeks after claiming, call the Self Assessment helpline on 0300 200 3310, Monday to Friday, 8am to 6pm.

Under Making Tax Digital

Once you are in Making Tax Digital for Income Tax (MTD), HMRC adds the CIS deductions it holds to your MTD tax return, and any refund is requested separately through HMRC online services. GOV.UK says you cannot claim it in the MTD tax return itself, so nothing is requested until you, or an agent through its agent services account, ask for it. The free MTD check shows when MTD starts for you, and the trades section explains how we keep CIS deductions matched to your statements all year.