How Long Does It Take to Get a CIS Tax Refund

If you are a subcontractor working under the Construction Industry Scheme (CIS), you may have paid more tax than you owe. Since contractors deduct CIS tax at source, it is common for subcontractors to end up with an overpayment that must be reclaimed from HMRC. The good news is that you can claim a refund, but how long it takes depends on how and when you submit your return, as well as your business structure. This article explains how long CIS refunds usually take, what can delay them, and how to make sure your claim is processed as quickly as possible.

How CIS tax refunds work

Under the CIS system, contractors deduct tax from subcontractors’ payments and send it to HMRC. These deductions count as advance payments towards your final Income Tax or Corporation Tax bill.

However, because the deductions are made at a flat rate (20% for registered subcontractors or 30% for unregistered ones), they rarely match your actual tax liability.

For example, you might have legitimate business expenses such as tools, materials, and travel costs that reduce your taxable profit. When you submit your annual tax return, HMRC recalculates how much tax you owe and refunds any overpayment.

The refund process and timescale depend on whether you are self employed or operate as a limited company.

CIS refunds for self employed subcontractors

If you are a self employed subcontractor, your CIS tax refund is handled through your annual Self Assessment tax return.

Step 1: Submit your Self Assessment tax return

The refund process begins once you file your return. The earlier you file after the tax year ends on 5 April, the sooner HMRC can process your refund.

Most subcontractors can submit their return online using HMRC’s website or accounting software. You must include:

  • Your total income from CIS jobs.

  • The amount of tax deducted by each contractor.

  • Your allowable business expenses.

The CIS deductions shown on your contractors’ monthly statements are essential for this step, so keep them safe throughout the year.

Step 2: HMRC processes your return

Once you have submitted your Self Assessment, HMRC will review your figures and compare the tax you owe with the amount already deducted under CIS.

If you have overpaid, HMRC will issue a refund, usually by bank transfer or cheque.

Step 3: Refund timescale

Most CIS tax refunds for self employed workers are processed within two to three weeks if you file online and your return is accurate.

However, it can take longer during peak periods, especially between April and August when many subcontractors submit their returns.

If you file a paper return, processing may take up to eight to twelve weeks because HMRC must enter your data manually.

CIS refunds for limited companies

If you run your construction business through a limited company, the process for claiming a CIS refund is different because your company pays Corporation Tax and reports CIS deductions through PAYE.

Step 1: Report CIS deductions on payroll

Each month, your company must report CIS deductions made by contractors on an Employer Payment Summary (EPS). This tells HMRC how much tax has already been deducted and allows them to offset it against your PAYE and National Insurance liabilities.

If your CIS deductions exceed your PAYE liability, the excess can be carried forward to future months.

Step 2: Apply for a refund at the end of the tax year

At the end of the tax year (after 5 April), if your company still has CIS deductions left after offsetting PAYE, you can apply for a refund.

This can be done by:

  • Writing to HMRC’s CIS Refunds team.

  • Submitting a refund request through your company’s HMRC online account.

You will need to include your company’s name, PAYE reference, Unique Taxpayer Reference (UTR), and bank details. HMRC may ask for supporting evidence such as CIS deduction statements or payroll reports.

Step 3: Refund timescale for companies

CIS refunds for limited companies usually take six to eight weeks once HMRC receives your claim.

The delay is because HMRC must reconcile your company’s PAYE and CIS records before releasing the refund. If there are discrepancies or missing reports, the process can take longer.

In some cases, HMRC may contact you to verify details before processing the payment, which can add another few weeks.

Factors that can delay your CIS refund

Several factors can slow down your refund, including:

  • Errors on your tax return: Mistakes or missing figures can trigger manual reviews.

  • Incomplete CIS statements: HMRC may ask for proof of deductions.

  • Outstanding debts: If you owe other taxes, HMRC will offset your refund against these.

  • Paper submissions: These take longer to process than online filings.

  • Bank verification: If your bank details are incorrect, payments can be delayed or rejected.

To avoid delays, double-check all figures before submitting your return and ensure your bank details are up to date in your HMRC account.

How to check the status of your CIS refund

You can track your refund by logging in to your HMRC Personal Tax Account (for self employed subcontractors) or Business Tax Account (for limited companies).

The system will show whether your return has been received and whether a refund has been issued.

If it has been more than six weeks for a Self Assessment refund or twelve weeks for a limited company refund, you can contact HMRC’s CIS helpline to request an update.

How to speed up your refund

Here are some practical ways to make sure your refund is processed quickly:

  • File your return early, ideally soon after 5 April.

  • Submit your return online rather than on paper.

  • Keep all CIS deduction statements and receipts organised.

  • Use the correct UTR, PAYE, and CIS references on all forms.

  • Respond promptly to any HMRC queries or document requests.

Working with an accountant can also help, as they can file your return correctly the first time and liaise directly with HMRC to prevent delays.

How an accountant can help with your CIS refund

An accountant who specialises in CIS can simplify the entire refund process by:

  • Checking your CIS deduction statements for accuracy.

  • Calculating your correct tax position.

  • Submitting your Self Assessment or company refund claim.

  • Communicating with HMRC on your behalf.

  • Ensuring all deadlines and compliance requirements are met.

This reduces the risk of mistakes and ensures your refund arrives as quickly as possible.

Final thoughts

Most CIS tax refunds are processed within two to three weeks for self employed subcontractors and six to eight weeks for limited companies. However, errors, missing documents, or peak filing times can cause delays.

The best way to speed up your refund is to file early, check your information carefully, and keep accurate records throughout the year. If you are unsure about the process, working with a CIS accountant will help ensure you get back every penny you are owed without unnecessary delays.