If you’re a CIS subcontractor, you need to file a self assessment tax return every year. There isn’t an exception. The return is where you report your income, claim your expenses, and account for the CIS deductions already taken from your payments. This guide walks through the process.
Why do CIS subcontractors need self-assessment?
CIS deductions are advance payments toward your tax bill, not the final amount. HMRC does not know your full income, expenses, or personal allowance until you file a return. Self assessment is how you show HMRC your actual position for the year.
With PAYE employment, your employer deducts the right amount of tax each period using your tax code. CIS works differently. A flat deduction rate is taken from your labour income, without regard for your total annual earnings, personal allowance, or allowable expenses.
At the end of the tax year, you may have paid too much and get a refund, or too little and owe more. Self assessment is what sorts that out.
All CIS subcontractors, including sole traders, partnerships, and company directors who receive CIS-deducted payments, must file self assessment returns.
When do you register for self-assessment?
If you’re new to CIS self-employment, register for self assessment with HMRC by 5 October after the end of your first tax year. Missing the deadline means a penalty.
For example, if you started CIS work in September 2025, during the 2025-26 tax year, you must register for self assessment by 5 October 2026.
Register online through your HMRC Government Gateway account. Choose “Register for Self Assessment” and follow the steps. HMRC sends your Unique Taxpayer Reference (UTR) by post, which usually takes around 10 working days.
You cannot file a self assessment return without a UTR.
What are the self-assessment deadlines?
The tax year runs from 6 April to 5 April. These are the main self assessment deadlines for each tax year:
– 5 October: Register for self assessment, if you’re new to it
– 31 October: Deadline to file a paper return
– 31 January: Deadline to file an online return and pay any tax owed
– 31 July: Payment on Account deadline, if HMRC has asked you to make advance payments
The 31 January online deadline is the one most CIS workers use. Late filing penalty: £100 straight away, then more after 3 months, 6 months, and 12 months. Late payment interest also applies.
How do CIS deductions appear in the return?
In the self assessment return, you declare all your income from construction work. You then enter your CIS deductions suffered in the relevant box. HMRC credits the deductions against your income tax and Class 4 NIC bill.
For sole traders: go to the “Self-employment” section. Enter gross income from construction. Deduct allowable expenses (see CIS subcontractor expenses) to arrive at taxable profit. Then enter CIS deductions suffered under “tax deducted” in the tax calculation section.
For partnerships: each partner declares their share of partnership income on their individual return.
For companies: the company files a Corporation Tax return (CT600), not a self assessment return. CIS deductions suffered by the company appear on the CT600.
How do you know how much CIS was deducted?
Every contractor who paid you must have given you a CIS payment and deduction statement with each payment. Add up the deduction amounts shown on all statements for the tax year. That total is your CIS deductions suffered.
Keep all statements. HMRC cross-checks your self assessment figures against the monthly returns filed by the contractors who paid you. If the numbers do not match, HMRC may ask questions.
If you lost any statements, contact the contractors who paid you and ask for duplicates. They are required to keep records for three years.
What if CIS deductions exceed the tax you owe?
If your CIS deductions are higher than your final income tax and NIC liability, HMRC refunds the difference. This happens when earnings are lower than expected, when you claim significant allowable expenses, or when you had gaps in work during the year.
HMRC usually processes self assessment refunds online within days of the return being processed. If you included bank details in the return, the refund goes straight into your account.
For more on claiming back overpaid deductions, see the CIS tax refund guide.
Payment on Account – what is it?
If your self assessment tax bill is more than £1,000 and less than 80% was collected through deduction at source, HMRC asks you to make “Payments on Account”, advance payments toward next year’s tax bill.
Payments on Account are split into two parts: 31 January, the same date as the main deadline, and 31 July. Each payment is 50% of the previous year’s tax bill.
CIS subcontractors with higher income often trigger Payments on Account. The first time it happens, it can feel like you are paying twice, one payment for the current year and one advance for next year, both due in January. Budget for it.
Can you avoid self-assessment by using umbrella PAYE?
Yes. Umbrella contractors are PAYE employees. Their tax is deducted accurately each month. They do not need to file self assessment unless they have other income. That is one reason some construction workers switch to an umbrella company: it removes the self assessment obligation entirely.
See how CIS works for a full picture of CIS versus umbrella PAYE.
