Self Assessment is how CIS subcontractors report income, claim expenses, and get their refund. This guide walks you through every section of the SA100 and SA103S — which boxes to fill in, where to enter CIS deductions (Box 21), the gross vs net mistake that catches everyone, and the deadlines that matter for 2025/26.

How to Fill In Your Self Assessment as a CIS Subcontractor: Step-by-Step Guide (2025/26)

QuoteDone · CIS Tax Guides

How to Fill In Your Self Assessment as a CIS Subcontractor: A Step-by-Step Guide

Published by QuoteDone Editorial Team · Aligned to HMRC 2025/26 Tax Year

Self Assessment is how CIS subcontractors report their income, claim expenses, and get their refund. If you've never filed before — or if you've been putting it off — this guide walks you through every section, every box, and every deadline.

31 Jan 2027 Online filing deadline for 2025/26

SA103S Self-employment form (under £90K)

Box 38 Where CIS deductions go (SA103S)

Filing Self Assessment is the only way to get your CIS money back from HMRC. Every pound that was deducted from your payments during the year — the 20% (or 30%) your contractor withheld — sits with HMRC until you file your return and prove what you actually owe.

For most CIS subcontractors, filing results in a refund. The flat CIS deduction doesn't account for your personal allowance or your business expenses, which means more was deducted than you actually owe. But you only get that money back by completing Self Assessment.

If the form looks intimidating, it isn't — once you know which pages apply to you and which boxes to fill in. For a typical CIS subcontractor, you're completing the SA100 (main return) and the SA103S (self-employment short pages). That's it.

"Self Assessment isn't complicated for most CIS subcontractors. It's SA100 plus SA103S — your income, your expenses, your CIS deductions. Three things. The form just spreads them across several boxes."

— QuoteDone CIS Tax Guides

What You Need Before You Start

Your UTR (Unique Taxpayer Reference) — the 10-digit number HMRC issued when you registered. Don't have one? Read our UTR guide.
Government Gateway login — your 12-digit user ID and password for HMRC's online service
CIS payment and deduction statements — from every contractor you worked for during the tax year (6 April 2025 to 5 April 2026). What's on a deduction statement?
Records of all business expenses — receipts, mileage logs, insurance documents, phone bills
Bank statements — showing CIS payments received (for cross-referencing)
P60 or P45 — if you also had PAYE employment during the year
Your bank account details — so HMRC can pay your refund directly

Which Form Do You Need?

Every CIS subcontractor files the SA100 (the main tax return) plus supplementary pages for self-employment income:

Self Assessment Forms for CIS Subcontractors

SA100 Main tax return — personal details, allowances, summary

SA103S (Short) Self-employment pages — if turnover under £90,000

SA103F (Full) Self-employment pages — if turnover £90,000+

SA102 Only if you also had PAYE employment

Most CIS subcontractors use SA100 + SA103S. If you file online (which you should — it's faster and gives you until 31 January), HMRC's system automatically selects the right supplementary pages based on the questions it asks. You don't need to download separate forms.

🚫 CIS Income Goes on SA103 — NOT SA102 Your CIS self-employment income must be entered on the self-employment pages (SA103S or SA103F). It does not go on the employment pages (SA102). This is one of the most common mistakes — CIS subcontractors are self-employed, not employees, even though tax is deducted at source. Putting CIS income on SA102 will result in incorrect calculations and potential HMRC queries.

Filling In Your Return — Section by Section

Step 1: SA100 — Personal Details and Income Sources

The SA100 starts with your personal information — HMRC pre-populates most of this if you file online. Check that your name, address, UTR, and National Insurance number are correct.

You'll then tick boxes to indicate which types of income you have. For a typical CIS subcontractor, tick "self-employment". If you also had a PAYE job, tick "employment" as well. HMRC will add the relevant supplementary pages.

Step 2: SA103S — Your CIS Income (Turnover)

This is the most important section. The self-employment pages ask for your business income and expenses.

Turnover (Box 9 on SA103S)

Enter your gross CIS income — the total amount you invoiced before CIS deductions were taken. This is your turnover, not the net amount that landed in your bank. Add up the "gross amount" column from all your CIS payment and deduction statements.

⚠️ Gross — Not Net This is the mistake that causes the most problems. If you earned £40,000 gross and £8,000 was deducted, your turnover is £40,000 — not £32,000. The deductions are entered separately in a different box. Entering the net amount means your income is understated, your expenses look disproportionately high, and HMRC may query your return.

Step 3: SA103S — Your Business Expenses

The SA103S has individual boxes for different categories of expenses:

SA103S Expense Boxes — What Goes Where

Box 11 — Cost of goods bought for resale or materials Materials you supplied (not reimbursed)

Box 12 — Car, van, and travel expenses Mileage at 55p/mile or actual vehicle costs

Box 13 — Wages, salaries, and staff costs If you employed anyone (rare for sole traders)

Box 14 — Rent, rates, power, and insurance Public liability insurance, premises costs

Box 15 — Repairs and maintenance Tool repairs, equipment maintenance

Box 16 — Accountancy and professional fees What you pay your accountant

Box 17 — Interest and bank charges Business bank fees

Box 18 — Phone, fax, stationery, office costs Business proportion of phone bill

Box 19 — Other allowable expenses PPE, workwear, CSCS card, training, use of home

Add them all up — the total goes in Box 20. The system calculates your net profit (Box 21) automatically: turnover minus expenses.

Step 4: Enter Your CIS Deductions — The Refund Box

This is the box that triggers your refund:

CIS Deductions (SA103S)

Box 38 — "Total Construction Industry Scheme (CIS) deductions taken from your payments by contractors". Enter the total of all CIS deductions from all your payment and deduction statements for the year. On the full form SA103F, this is Box 82.

HMRC takes this number and offsets it against your total tax liability. If the deductions exceed what you owe, the difference is your refund.

How Your Refund Is Calculated

Gross CIS income (Box 9) £40,000

Total expenses (Box 20) £6,000

Net profit (Box 21) £34,000

Personal allowance £12,570

Taxable income £21,430

Income tax owed (20%) £4,286

Class 4 NIC (6% on £12,570–£50,270) £1,286

Total tax + NI liability £5,572

CIS already deducted and paid to HMRC £8,000

Your refund £2,428

✓ No registration required · 100% Free · HMRC 2026/27 Aligned

Step 5: Add Your Bank Details

HMRC pays refunds directly to your bank account — but only if you provide your details on the return. There's a section near the end of the SA100 for bank account name, sort code, and account number. Fill this in. If you leave it blank, HMRC sends a cheque by post, which takes significantly longer.

Step 6: Review and Submit

Before submitting, HMRC's online system shows you a summary of your return and calculates your tax position — either tax to pay or a refund due. Check the figures against your records. If everything matches, submit. You'll receive an acknowledgement with a reference number — save it.

Making Tax Digital — If Your Income Is Over £50,000

From April 2026, self-employed individuals and landlords with qualifying income above £50,000 must use Making Tax Digital for Income Tax. This means quarterly digital updates to HMRC using compatible software, in addition to an annual final declaration (which replaces the traditional Self Assessment return).

⚠️ MTD Doesn't Change How CIS Deductions Work Even under MTD, your CIS deductions are still offset against your total tax liability. The difference is that you report income and expenses quarterly rather than annually. If your gross CIS income is below £50,000, MTD doesn't apply to you yet — you continue filing Self Assessment as normal. The threshold drops to £30,000 from April 2027.

Key Deadlines for 2025/26

Date	What Happens
5 April 2026	2025/26 tax year ends
6 April 2026	You can start filing your 2025/26 return
5 October 2026	Deadline to register for Self Assessment (new filers)
31 October 2026	Paper return deadline
31 January 2027	Online return deadline + payment deadline

✅ File Early — Get Paid Early You don't have to wait until January. File your return as soon as the tax year ends in April and your refund could arrive in May or June — instead of February or March. HMRC processes early returns faster because there's no queue. Filing early doesn't mean you pay earlier — you still have until 31 January to pay any tax owed.

What Happens If You Owe Tax (Payments on Account)

If your Self Assessment shows you owe more than £1,000 in tax and less than 80% was collected through CIS deductions, HMRC may require Payments on Account — advance payments toward next year's tax bill. These are split 50/50 between 31 January and 31 July.

This catches many first-time filers off guard. You file for 2025/26, and suddenly you owe not just the balance for that year, but also a 50% advance for 2026/27. It's designed to spread your tax payments, but the first year feels like a double bill.

Late Filing Penalties

What Happens If You Miss the Deadline

1 day late £100 penalty (even if you owe nothing)

3 months late £10 per day (up to 90 days = £900)

6 months late £300 or 5% of tax due (whichever is higher)

12 months late Another £300 or 5% of tax due

The penalties apply even if HMRC owes you a refund. Filing late to claim back £3,000 while paying £100 in penalties is still worth it — but filing on time costs you nothing.

Your Self Assessment Filing Checklist

Gather all CIS payment and deduction statements for the year
Add up your gross CIS income (turnover) from all statements
Add up your total CIS deductions from all statements
Collect all business expense receipts and records
Log in to HMRC via Government Gateway
Complete SA100 personal details section
Complete SA103S: enter gross income (Box 9), expenses (Boxes 11–19), CIS deductions (Box 38)
Enter your bank details for refund payment
Review the summary — does the refund/tax figure look right?
Submit and save your acknowledgement reference

Frequently Asked Questions

Do I need an accountant to file my Self Assessment?

No — you can file yourself through HMRC's online service. It's free and walks you through the questions step by step. However, an accountant can identify expenses you might miss and ensure your return is accurate, which can increase your refund. If your affairs are simple (one self-employment, no other income), doing it yourself is straightforward.

What if I worked for multiple contractors?

Add up the gross income and CIS deductions from all contractors — your SA103S covers your total self-employment income, not individual jobs. You enter one total turnover figure and one total CIS deduction figure. Keep all deduction statements from every contractor as your evidence.

Can I file if I don't have all my deduction statements?

You should have all your statements before filing. If you're missing some, contact the contractor first, then HMRC's CIS helpline on 0300 200 3210. Filing with incorrect CIS deduction figures will cause a mismatch with HMRC's records and may delay or block your refund. Don't estimate — get the actual figures.

I also have a PAYE job. How does that affect my return?

Your PAYE income is reported on the employment pages (SA102), which is separate from your CIS self-employment pages (SA103S). HMRC combines both incomes to calculate your total tax liability. Your CIS deductions are still offset against the total — but your personal allowance may already be used up by your PAYE income, which affects how much CIS refund you're owed.

Ready to File? Check Your Numbers First.

Estimate your CIS refund before you file and make sure every invoice has labour and materials separated correctly.

CIS Refund Calculator Ready to claim your CIS refund? Use our free calculator to find out what HMRC owes you. CHECK YOUR REFUND NOW →

Free Invoice Generator Need professional invoices fast? Create clean, compliant invoices in seconds with our free tool. TRY FREE INVOICE GENERATOR →

This article is for informational purposes only and does not constitute formal tax, financial, or legal advice. Self Assessment rules, box numbers, and deadlines may change between tax years. Always check the current year's notes on gov.uk or consult a qualified accountant. Aligned to 2025/26 tax year guidance.

How to Fill In Your Self Assessment as a CIS Subcontractor: Step-by-Step