How Long Does It Take to Get a CIS Tax Refund

At Towerstone Accountants we provide specialist CIS accountancy services for contractors, subcontractors, and construction businesses across the UK. We created this webpage for people working in construction who want clear guidance on CIS deductions, refunds, verification, and monthly return responsibilities, without jargon. Our aim is to help you stay compliant with HMRC, avoid penalties, and keep your cash flow and records under control.

This is one of the most common and most frustrating questions I hear from CIS subcontractors. You know tax has been deducted from your payments all year, you are fairly confident you are due money back, yet once the tax return is submitted everything seems to slow down. Days turn into weeks, weeks turn into months, and it can start to feel like your refund has disappeared into a black hole.

In my experience CIS refunds are rarely delayed for no reason. HMRC does not process CIS refunds in quite the same way as many other tax repayments, and understanding what actually happens behind the scenes makes the waiting far less mysterious and far easier to plan around.

In this article I am going to explain how long a CIS tax refund typically takes, what affects the timing, why some refunds arrive quickly while others drag on, and what you can do to reduce delays. I will also explain the difference between sole trader and limited company refunds, because the timelines are not always the same. By the end you should have a realistic expectation of timing rather than guesswork or false hope.

What a CIS tax refund actually is

Before looking at timescales it helps to clarify what a CIS tax refund actually represents.

A CIS refund is not a special payment separate from your tax return. It is simply the repayment of tax that has already been deducted at source under the Construction Industry Scheme and has turned out to be more than your final tax liability.

For sole traders and partners this refund usually arises through the Self Assessment process. For limited companies it usually arises through the Corporation Tax return or PAYE account.

The refund only exists once HMRC has calculated your final tax position, which is why timing always starts with the relevant return being submitted and processed.

Typical CIS refund timescales for sole traders

For sole traders the most common route to a CIS refund is through the annual Self Assessment tax return.

Once the return has been submitted online and accepted by HMRC, the typical processing time for a straightforward refund is around two to four weeks. In some cases it can be quicker, particularly outside peak periods, but two to four weeks is a realistic expectation when everything is clean and matches HMRC’s records.

However that timeframe assumes there are no discrepancies, no missing CIS statements, and no additional checks triggered. Where those issues exist, the timescale extends significantly.

Why some CIS refunds arrive faster than others

When a CIS refund is processed quickly it is usually because HMRC’s systems can automatically match what you have claimed to what contractors have reported.

Every contractor you work for submits monthly CIS returns showing what they have paid you and what they have deducted. HMRC uses those returns to build a picture of your CIS position.

If your tax return matches that picture closely, the system has no reason to pause. The refund moves through automatically and payment is released.

This is why some people receive refunds surprisingly quickly, while others wait much longer.

Common reasons CIS refunds are delayed

Most delays fall into a small number of categories.

The most common issue is missing or incorrect CIS deduction information. If the deductions you claim on your tax return do not match what contractors have reported, HMRC cannot reconcile the figures automatically.

Name mismatches are another frequent problem. Something as small as a trading name being used on one system and a personal name on another can prevent matching.

Timing issues also play a role. Contractors submit CIS returns monthly, and if a contractor has submitted late or made corrections, HMRC’s records may not yet reflect the deductions you are claiming.

Any of these issues can push a refund out of the automatic process and into manual review, which is where delays increase.

HMRC security and compliance checks

CIS refunds are considered higher risk than some other repayments, because the tax has been paid by third parties rather than directly by the person claiming the refund.

As a result HMRC sometimes applies additional security or compliance checks, even where figures appear broadly correct.

These checks can add several weeks to the process. In some cases HMRC may write to ask for copies of CIS statements or confirmation of income figures.

While frustrating, these checks are not accusations. They are simply part of HMRC’s risk management approach.

How the time of year affects CIS refunds

Timing during the tax year makes a real difference.

January to April is the busiest period for Self Assessment processing. HMRC systems are under heavy load, and refunds submitted during this period often take longer than those submitted earlier in the year.

By contrast refunds submitted in late spring or summer are often processed more quickly, because there is less pressure on the system.

This does not mean you should delay submitting your return if it is ready, but it does mean expectations should be adjusted depending on when submission happens.

How long CIS refunds take if HMRC asks questions

If HMRC raises a query, the clock effectively resets.

Once a query is issued, the refund will not be paid until the query is resolved and HMRC is satisfied. The speed then depends on how quickly and how clearly the query is answered.

In practice I see queries resolved anywhere from two weeks to several months, depending on the quality of information provided and whether further clarification is needed.

This is one of the reasons why preparation before submission matters so much.

CIS refunds for partnerships

For partnerships the process is similar to sole traders but slightly more layered.

The partnership return must be processed first, and then each partner’s personal tax return is processed. CIS deductions are allocated between partners and offset against their individual tax bills.

Refunds are therefore dependent on both returns being correct and aligned. Any mismatch between the partnership figures and individual claims can delay processing.

As a result partnership CIS refunds often take slightly longer than sole trader refunds, particularly where there are multiple partners.

CIS refunds for limited companies

Limited company CIS refunds follow a different path and often a different timeline.

When a limited company suffers CIS deductions, those deductions are offset against Corporation Tax or PAYE liabilities. In some cases this results in a refund, in others it results in a credit that reduces future payments.

Corporation Tax returns are generally processed more slowly than Self Assessment returns, and refunds can take several weeks or longer after the return has been finalised.

In my experience limited company CIS refunds commonly take four to eight weeks once the Corporation Tax position is agreed, sometimes longer where PAYE offsets are involved.

Why limited company refunds can sit unnoticed

One issue I see regularly is limited companies building up CIS credits without realising it.

Because the deductions do not automatically trigger a cash refund, they can sit on HMRC systems as credits, offsetting liabilities gradually rather than being repaid.

Unless someone actively reviews the position and requests a refund or offset, the company may never see the cash.

This is less about delay and more about awareness, but it often feels like the refund is missing.

How payments on account affect refund timing

For sole traders, payments on account can complicate the picture.

Even where a CIS refund is due for the year just ended, HMRC may offset that refund against payments on account for the following year.

This means you may not receive a cash payment even though your return shows a refund. Instead the amount is used to reduce future tax bills.

This often causes confusion and leads people to believe their refund is delayed, when in reality it has been applied elsewhere.

What happens after the return is processed

Once HMRC has processed your return and agreed the figures, the refund is issued.

For individuals this is usually paid directly to your bank account if details are on file, or by cheque if not. Bank payments are faster and more reliable.

For companies the refund may be issued to the company bank account or reflected as a credit on the HMRC account.

From this point payment is usually made within a few working days, assuming there are no offsets against other liabilities.

How long refunds take once approved

Once a CIS refund is approved, payment is usually quite quick.

Bank repayments are often made within three to five working days. Cheques take longer, typically up to ten working days once issued.

This is why most of the waiting happens before approval rather than after.

What you can do to speed up a CIS refund

While you cannot control HMRC processing times entirely, there are steps that significantly reduce delays.

Ensuring CIS registration details are correct and consistent across contractors is one of the most important.

Keeping all CIS deduction statements and reconciling them before submitting a return avoids mismatches.

Submitting a complete and accurate return, rather than rushing and amending later, also makes a big difference.

Finally, making sure there are no outstanding returns or unpaid liabilities elsewhere on your HMRC account helps prevent offsets or holds.

Why chasing HMRC too early rarely helps

I understand the temptation to chase HMRC as soon as a refund feels late, but in the early stages it rarely speeds things up.

If a refund is still within the normal processing window, HMRC will usually not escalate it.

Chasing becomes more effective once the refund is clearly outside expected timescales or where a specific query has been raised and not progressed.

Knowing when to chase and when to wait saves time and stress.

How an accountant helps manage timing expectations

One of the less obvious benefits of using an accountant is clarity around timing.

Rather than vague estimates, an accountant can usually tell you whether a refund is likely to be quick, delayed, or offset, based on how the return has been prepared and your past history.

This replaces uncertainty with realistic planning, which is often more valuable than speed alone.

Realistic timelines to keep in mind

As a general guide, assuming everything is correct and straightforward:.

Sole trader CIS refunds often take two to four weeks after submission.
Refunds submitted during busy periods may take four to six weeks.
Limited company CIS refunds often take four to eight weeks after the Corporation Tax position is finalised.
Refunds involving queries or mismatches can take several months.

These are not guarantees, but they are grounded in what I see in practice.

Why patience and preparation go together

CIS refunds test patience, but preparation shortens the test.

Most long delays are not about HMRC being slow, but about HMRC needing to resolve uncertainty. The less uncertainty there is, the faster the process moves.

This is why the fastest refunds are usually the quietest, nothing unusual, nothing missing, nothing to question.

Final thoughts

So how long does it take to get a CIS tax refund. The honest answer is that it depends, but not in a random way.

When records are complete, figures align, and returns are prepared properly, refunds often arrive within a few weeks. When information is missing or inconsistent, delays follow, sometimes stretching into months.

From my experience the key is not hoping for speed, but creating the conditions where speed is possible. Once you understand how HMRC processes CIS refunds and what slows them down, the waiting becomes far more predictable and far less stressful.

Handled properly, a CIS refund stops feeling like a mystery and becomes just another part of the tax cycle, one that you can plan around rather than worry about.

You may also find our guidance on How do CIS tax refunds work for subcontractors and How can an accountant help me claim my CIS refund faster helpful when dealing with related CIS questions. For a broader overview of CIS rules, compliance, and support, you can visit our cis guidance hub.