Why HMRC holds a Self Assessment repayment for checks

Q: What can you do to get the money released?

Check the status first. Sign in to the online account and look at the repayment. "Pending" means it exists and is waiting for approval, not that it has been refused. Use the reply tool before chasing. If the expected time has not passed, a call is unlikely to speed things up. Ask for the full amount if it was reduced. SAM110020 says that where a repayment was reduced to cover a bill becoming due, the full amount can be repaid if you ask before that bill's due date. Check the bank details on the return. HMRC takes the account and any nominee details from the return, so an error there causes avoidable problems. If the refund is being paid to an agent, see nominating repayments to an agent. Answer any HMRC request quickly and fully. If an officer writes asking you to confirm details or provide evidence, a complete reply is the fastest way to get the check closed. Find out whether a debt is involved. If HMRC has used the repayment against another tax, the rules in HMRC set off of repayments apply. Complain if the delay is unreasonable. GOV.UK lists delays in processing as a valid service complaint. HMRC reviews it as a first tier complaint and will consider refunding reasonable costs directly caused by its mistakes or delays, including professional fees. The route to the Adjudicator is explained in HMRC complaints and the Adjudicator.

Q: What does this look like in practice?

Illustration only. Priya files her return in mid December showing an overpayment of £3,000. A payment on account of £1,200 for the following year falls due on 31 January, which is within 45 days, so the system drafts a repayment of £1,800 and keeps the rest to cover the payment on account. The draft is then selected by the risk criteria and her online account shows it as pending. Priya checks the reply tool, waits for the stated period and then calls. HMRC asks her to confirm a figure on the return, which she does the same day, and the repayment is authorised and paid shortly afterwards with repayment interest. Because she also asked before 31 January for the £1,200, SAM110020 allows that to be repaid too, although she then needs to pay the payment on account herself by the due date.

Most Self Assessment repayments are issued automatically, but every draft repayment is first tested against HMRC’s pre repayment risk criteria, and some are pulled out for security checks and manual authorisation before any money is sent. Others are held back by signals on the taxpayer’s record, such as a payment that has not yet cleared, a debt or a bill falling due within 45 days. HMRC publishes no fixed time limit for these checks, so the practical route is to confirm the status, give HMRC what it needs quickly and escalate if the delay becomes unreasonable.

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How does HMRC decide whether to release a repayment straight away?

When a return asking for a repayment is captured, HMRC’s system looks at the whole Self Assessment account rather than the return in isolation. The Self Assessment Manual at SAM110020 explains that it takes into account the overall balance, liabilities that are about to become due, payments made in the last 14 days that have not cleared, and any balancing charge from a return that is not yet due. Where £10 or more is available and nothing is blocking a repayment, the system creates a draft repayment.

The same page says every draft repayment is run against the “pre repayment risk criteria” and may be selected for detailed pre issue security checks followed by manual authorisation or cancellation. A repayment that is not selected is authorised automatically. Once authorised, the Self Assessment Repayment System issues it within 3 days, and HMRC expects the taxpayer to receive it within 5 days of authorisation, although a bank transfer can take a little longer to reach the account.

HMRC’s general approach, set out in the Enquiry Manual at EM1609, is “process now, check later”: the repayment is normally made and any questions follow. Pre issue checks are the exception, used where the risk is high enough that HMRC wants to verify before paying.

What can cause a repayment to be held?

A held repayment is not always the result of a risk check. SAM110205 lists the circumstances in which an automatic repayment is inhibited and sent to a work list for an officer to review:

the taxpayer is insolvent, or a priority collection action signal is set
the taxpayer has died and HMRC holds no details of who is acting for the estate
post to the taxpayer’s address has been returned undelivered
a “no repayment” signal has been set
an uncleared payment, a remission or an informal standover is recorded on the account
a payable order would exceed £150,000

SAM110125 explains that the “no repayment” signal is set automatically when a section 9A enquiry into the return is registered, and can be set manually for reasons including a processing error that could produce an incorrect repayment, an outstanding debt or a deed of assignment. It adds that a repayment should not be blocked just because the taxpayer has other returns outstanding.

Size also counts. Under SAM110140, repayments of £250,000 or more go through more robust security checks whatever method is used to pay them. Separately, GOV.UK warns that you may not get a refund if you have tax due in the next 45 days, such as a payment on account, because the money is used against that bill instead.

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Why would HMRC check a repayment before paying it?

EM1609 gives HMRC’s own examples of when it may verify a claim before repaying. They include cases where there is reason to doubt the bona fides of the claim or the claimant, where the repayment risk assessment has flagged problem areas, where there is reasonable doubt that some or all of the repayment is due, where the amount is disproportionate to the claimant’s apparent means, and where there is doubt that the money could be recovered if it later proved not to be due. Repayments generated by an avoidance scheme are also mentioned.

The same guidance draws a clear line. If an officer intends to withhold all or part of a repayment, they must open an enquiry into the return. A security check therefore cannot become an open ended hold: once HMRC decides it is not going to pay, the formal enquiry rules apply. Those rules are covered in Can HMRC hold a repayment during an enquiry.

How long can the checks take?

HMRC does not publish a fixed period for pre issue security checks. Its “Check when you can expect a reply from HMRC” tool covers Self Assessment and is updated weekly, so it is the best guide to current processing times before you chase. While a repayment is being checked, your online account may show its status as “pending”, which GOV.UK explains means the refund has been created but still needs to be approved and paid.

The delay is at least partly compensated. The Self Assessment Legal Framework at SALF306 explains that repayment interest runs from the repayment interest start date (generally the later of the date the tax was paid and the date it was due) until the date the repayment is made. HMRC’s published rate is the Bank of England base rate minus 1%, with a floor of 0.5%, and section 749 of the Income Tax (Trading and Other Income) Act 2005 makes repayment interest free of income tax. More detail is in HMRC repayments and repayment interest.

What can you do to get the money released?

Check the status first. Sign in to the online account and look at the repayment. “Pending” means it exists and is waiting for approval, not that it has been refused.
Use the reply tool before chasing. If the expected time has not passed, a call is unlikely to speed things up.
Ask for the full amount if it was reduced. SAM110020 says that where a repayment was reduced to cover a bill becoming due, the full amount can be repaid if you ask before that bill’s due date.
Check the bank details on the return. HMRC takes the account and any nominee details from the return, so an error there causes avoidable problems. If the refund is being paid to an agent, see nominating repayments to an agent.
Answer any HMRC request quickly and fully. If an officer writes asking you to confirm details or provide evidence, a complete reply is the fastest way to get the check closed.
Find out whether a debt is involved. If HMRC has used the repayment against another tax, the rules in HMRC set off of repayments apply.
Complain if the delay is unreasonable. GOV.UK lists delays in processing as a valid service complaint. HMRC reviews it as a first tier complaint and will consider refunding reasonable costs directly caused by its mistakes or delays, including professional fees. The route to the Adjudicator is explained in HMRC complaints and the Adjudicator.

What happens if HMRC opens an enquiry instead?

Once an enquiry into the return is open, section 59B(4A) of the Taxes Management Act 1970 applies. HMRC does not have to make the repayment until the enquiry is completed by a final closure notice, although the officer may make a provisional repayment of as much as they think fit. If the enquiry drags on, you can apply to the tribunal under section 28A(4) for a direction requiring HMRC to issue a closure notice within a set period. See HMRC closure notices for how that process works.

What does this look like in practice?

Illustration only. Priya files her return in mid December showing an overpayment of £3,000. A payment on account of £1,200 for the following year falls due on 31 January, which is within 45 days, so the system drafts a repayment of £1,800 and keeps the rest to cover the payment on account. The draft is then selected by the risk criteria and her online account shows it as pending.

Priya checks the reply tool, waits for the stated period and then calls. HMRC asks her to confirm a figure on the return, which she does the same day, and the repayment is authorised and paid shortly afterwards with repayment interest. Because she also asked before 31 January for the £1,200, SAM110020 allows that to be repaid too, although she then needs to pay the payment on account herself by the due date.

What mistakes cause the longest delays?

Chasing before the published processing time, which rarely moves a case forward.
Treating “pending” as a refusal and filing an amended return, which can trigger further processing.
Ignoring a letter asking for confirmation because it looks routine.
Using a complaint to dispute the amount of tax. GOV.UK says decisions about tax, penalties or relief need an appeal or review, not a complaint.
Assuming outstanding returns for other years are the reason for the hold. SAM110125 says that alone should not block a repayment, so ask HMRC what the actual reason is.

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Reviewed by Christine Anderson, Broker, Solar Protect. Last reviewed 24 October 2026. Part of Accountapedia, the Solar Protect guide to UK tax and accounting. This page is general information, not personalised advice.