The part people do not expect is that most of the wait happens before you file anything. Deductions are taken from April onwards, and nothing can be repaid until the tax year has ended. Here is the actual sequence.
The sequence
A sole trader recovers CIS deductions through the Self Assessment return, and that return cannot be filed until the tax year it covers has ended. So a deduction taken from a payment in April sits with HMRC for a full twelve months before the return that recovers it can even be submitted.
A deduction suffered in April 2026 falls in the tax year ending 5 April 2027. The return for that year can be filed from 6 April 2027 and is due by 31 January 2028. File it on the first day you can and the money has been with HMRC for twelve months. File it at the deadline and it has been there for twenty-two.
Once the return is submitted and the repayment is agreed, HMRC pays out. Straightforward claims filed online are usually dealt with in a matter of weeks. Several things extend that:
The way to shorten the wait is to file as soon as the tax year ends rather than in January. Nothing about the return gets easier by waiting, and the money is yours from 6 April.
For a labour-only subcontractor this is a permanent working-capital drag. The cash is taken continuously and returned once a year. There are two structural fixes. Gross payment status stops the deduction being made at all, so there is nothing to reclaim. If you trade through a company, running a real payroll lets you offset deductions monthly through the EPS instead of waiting — see CIS refunds for limited companies.
From 6 April, the day after the tax year ends. The Self Assessment return for a tax year cannot be filed until that year has finished, and the deductions cannot be set against your liability until the return is filed. The deadline for filing online is the following 31 January, but there is no advantage in waiting — the earlier you file, the earlier you are repaid.
A straightforward online claim with no complications is usually processed within a few weeks. Repayment claims are subject to security checks, and first or unusually large claims are more likely to be selected, which adds time. Providing bank details for a direct repayment is faster than a cheque.
The most common causes are a security check on the repayment, a mismatch between the deductions you have claimed and what your contractors reported to HMRC, an earlier year's return still outstanding, or tax owed elsewhere that the repayment has been set against. Your payment and deduction statements resolve the mismatch case, because they show what was deducted and on what basis.
Some refund companies offer to advance the money and recover it from the repayment. That is a credit arrangement and it has a cost, whether it is described as a fee or a deduction from the refund. Before taking one, work out what the charge amounts to against the number of weeks you would otherwise have waited, and check whether the agreement covers only this year or future years too.
If you are labour-only and in a repayment position every year, gross payment status is the fix. We will tell you whether you would pass the three tests.