Filing self assessment as a locum doctor is its own annual job, separate from simply earning the money. This locum doctor self assessment filing guide walks through the practical mechanics for 2026/27, from registering with HMRC and gathering records to completing the right pages, working out payments on account, and getting ready for Making Tax Digital. It is general information for UK locum GPs and consultants, not personal tax advice.

If you want the wider picture of how locum tax works, read our locum doctor tax complete guide first. This page is the step-by-step filing companion: what to put where, by when. For the detail of what you can deduct, see the locum doctor expenses guide rather than duplicating it here.

Do locum doctors have to file a self assessment return

Most freelance locums do. You need to complete a self assessment return for 2025/26 if any of the following apply:

  • You had self-employed locum turnover above the £1,000 trading allowance.
  • You had a mix of employed (PAYE) sessions and self-employed locum work.
  • You received income from several sources (NHS sessions, private clinics, agency work).
  • You had other untaxed income to report, for example rental profit, savings interest or dividends.
  • HMRC has issued you a notice to file.

This covers locum GPs, locum consultants and doctors picking up sessions through agencies or directly with practices. Even where some shifts are taxed through PAYE, the self-employed element normally still needs a return so the right amount of tax and National Insurance is settled across all your income.

Which self assessment pages a locum doctor completes

A freelance locum is usually a sole trader, so the return is built from the main form plus the self-employment supplement:

  • SA100: the main return, where total income, reliefs and the final calculation pull together.
  • SA103: the self-employment pages for your locum trade. Use the short version (SA103S) where turnover is modest and accounts are simple, or the full version (SA103F) where turnover is higher or the figures are more involved.
  • SA102: the employment pages, for any salaried GP role or PAYE locum sessions reported on a P60 or P45.
  • Other supplements as needed, for example UK property (SA105) for rental income.

If you trade through a personal service company instead of as a sole trader, the picture is different: the company files its own accounts and corporation tax return, and your personal self assessment reports the salary and dividends you draw from it. That route also brings in the off-payroll rules and the loss of NHS pension accrual on company income. We cover that in the locum doctor limited company pros and cons page, so this guide stays with the sole-trader filing route.

Key self assessment deadlines for 2025/26

The 2025/26 tax year ran from 6 April 2025 to 5 April 2026. Missing a deadline triggers automatic penalties whether or not you owe tax:

  • 5 October 2026: deadline to register for self assessment if this is your first return for 2025/26.
  • 31 October 2026: paper return deadline for 2025/26.
  • 31 January 2027: online return deadline, and the date any tax owed for 2025/26 must be paid.
  • 31 July 2027: second payment on account due, if you make payments on account.

Late filing starts at an automatic £100 penalty, with daily £10 charges after three months and further penalties at six and twelve months, plus interest on unpaid tax. A return filed one day late carries the same £100 as one filed two months late, so there is nothing to gain from cutting it fine.

Documents to gather before you start

Pull these together before opening the return. Good records also matter under Making Tax Digital (covered below), so it is worth setting up the habit now.

Income records

  • P60s and P45s from any employed or salaried positions.
  • Invoices raised to practices, hospitals and agencies.
  • Remittance advices and agency statements.
  • Bank statements showing locum payments received.
  • Records of any private, medico-legal or other income.

Expense records

  • GMC annual retention fee and Royal College or specialty membership.
  • Medical indemnity (MDU, MPS or MDDUS) for private and non-clinical cover.
  • BMA subscription where on HMRC's approved List 3.
  • CPD courses and training relevant to your current work.
  • Mileage logs for travel between work sites.
  • Apportioned phone, internet and home-office costs.

One point worth knowing for NHS GP sessions: clinical negligence for NHS general practice in England has been state-indemnified through the Clinical Negligence Scheme for General Practice since 1 April 2019, so your own paid indemnity is now mainly for private, non-clinical or regulatory cover. The deduction detail sits in the expenses guide.

Step-by-step filing process

Step 1: Register for self assessment

If this is your first return, register online at gov.uk by 5 October following the end of the tax year. HMRC issues your Unique Taxpayer Reference (UTR) by post, which can take a couple of weeks, and you cannot file without it. If you already file, you only need to keep your existing Government Gateway and UTR details to hand.

Step 2: Choose your filing method

Most locums file online through HMRC's service or commercial software. Online filing gives the later 31 January deadline, automatic calculations and immediate confirmation. Note that from 2026/27 many locums also need Making Tax Digital compatible software (see the MTD section), which changes how records are kept through the year.

Step 3: Complete the employment pages (SA102)

Enter PAYE income from your P60s and P45s, including any salaried GP role or employed locum sessions where tax was deducted at source. The tax already paid is credited in the final calculation.

Step 4: Complete the self-employment pages (SA103)

This is usually the main section for a locum. You will enter:

  • Total turnover (all locum income received in the year).
  • Allowable business expenses.
  • Your accounting basis (cash basis is the default for most sole traders).
  • A short business description, for example "medical locum services".

Cash basis records income and expenses when money actually moves, rather than when an invoice is raised. It suits most locums, though it is worth checking the right basis for your circumstances.

Step 5: Claim your expenses

Deduct costs incurred wholly and exclusively for your locum work against the self-employed income. In summary these include professional fees (GMC, Royal College, indemnity for private and non-clinical cover), business travel between sites, relevant CPD, equipment and an apportioned share of phone and home-office costs. On motoring, HMRC's approved mileage allowance is 55p per mile for the first 10,000 business miles in 2026/27 (it rose from 45p on 6 April 2026) and 25p per mile thereafter; travel from home to a regular workplace is non-deductible commuting. The full list, with the medical-specific nuances, is in the expenses guide.

Step 6: Add other income and reliefs

Report any other income on the right pages: rental profit, savings interest, dividends or private medical work. Then claim eligible reliefs, for example personal pension contributions or Gift Aid donations. If you are an NHS scheme member, your NHS pension contributions are dealt with differently from a private pension, so check our NHS pension for locums Form A and Form B guide for how locum pensioning works.

Step 7: Review, submit and pay

Check every figure, let the system calculate the liability, then submit and pay any tax due by 31 January. Keep a copy of the filed return and the payment confirmation.

Class 4 National Insurance and the final calculation

Your self assessment also collects National Insurance on self-employed profit. For 2025/26, Class 4 NIC is 6% on profits between £12,570 and £50,270, then 2% above £50,270. The 6% main rate replaced the old 9% rate from 6 April 2024, so an older guide quoting 9% is out of date. Class 2 NIC is no longer a required weekly payment from 6 April 2024: if your profits are at or above the Small Profits Threshold you are treated as having paid and keep your state-pension entitlement, so there is no Class 2 charge to budget for (those below the threshold can still pay voluntarily). Income tax then applies on top through the usual bands, after your personal allowance.

Payments on account

If your self assessment bill is more than £1,000, and less than 80% of your tax was collected at source, HMRC asks for payments on account towards the following year. Each instalment is half of the current year's liability, due on 31 January and 31 July.

As a general illustration only, suppose a locum's 2025/26 bill works out at £8,000. On 31 January 2027 they pay the £8,000 balancing payment plus a £4,000 first payment on account for 2026/27, then a second £4,000 payment on account on 31 July 2027. When the 2026/27 return is filed, those payments on account are set against the actual bill and any difference is balanced. If your income has genuinely dropped you can apply to reduce the payments, but underestimating leaves interest to pay, so reduce only on a realistic forecast.

Making Tax Digital for Income Tax from April 2026

This is the biggest filing change for locums and the one most worth getting ahead of. Making Tax Digital for Income Tax (MTD for ITSA) started on 6 April 2026 for sole traders and landlords with qualifying income over a threshold that phases in:

  • £50,000 qualifying income, from 6 April 2026.
  • £30,000 qualifying income, from 6 April 2027.
  • £20,000 qualifying income, from 6 April 2028.

Qualifying income is your gross trading plus property income, tested on the relevant prior-year return. In practice most full-time locums exceed £50,000 and are in scope from 6 April 2026. Being in MTD means keeping digital records in compatible software and sending quarterly updates through the year, followed by a final declaration after the year-end, rather than a single annual return from memory.

Two carve-outs matter for doctors. Limited companies are outside MTD for ITSA (it is an income tax regime), so a locum trading through a personal service company is not brought in by it. And general partnerships are deferred with no confirmed date, so a GP partnership is not mandated at partnership level yet, although a partner's own sole-trader private work can still bring their personal return into MTD. If your income sits near £50,000, it is worth checking each year whether the prior-year figure tips you in.

IR35 and your filing position

A sole-trader locum has no intermediary company, so IR35 (the off-payroll rules) does not apply and your status is judged on the usual employed-versus-self-employed factors. IR35 only bites where you work through a personal service company. In that case the hirer normally decides your status: an NHS Trust or other public body decides for its engagements (and the fee-payer deducts PAYE on inside-IR35 work), a medium or large private hospital does the same and issues a Status Determination Statement, and only a small private client leaves the decision with your own company. IR35 has not been abolished, so you cannot assume it does not apply to NHS work. Across several hirers you can hold a mix of inside and outside determinations, and each must be reflected correctly.

VAT: usually not an issue, but worth a check

Clinical care by a registered medical practitioner is generally exempt from VAT, and NHS GMS or PMS income is outside the scope, so most locum income does not count towards VAT registration. The VAT registration threshold is £90,000 of taxable (non-exempt) turnover (raised from £85,000 on 1 April 2024), with deregistration at £88,000. Standard-rated work, such as purely cosmetic procedures or medico-legal and expert-witness reports, is what can build towards that threshold, so a locum with a significant non-clinical side income should keep an eye on it.

Common mistakes to avoid

  • Mixing business and personal costs: claim only what is wholly and exclusively for the locum work.
  • Out-of-date figures: use the 6% Class 4 rate, no Class 2 weekly charge, and the 55p first-10,000-mile rate for 2026/27, not older numbers.
  • Forgetting payments on account: the 31 January bill can be larger than expected because it includes the first payment on account.
  • Missing income: include every source, including small agency payments and private work.
  • Leaving MTD too late: if you are over £50,000, set up compatible software before the quarterly updates fall due.
  • Assuming IR35 never applies: if you use a company, check each engagement's determination.

Record keeping

Keep your self-employment records for at least five years after the 31 January filing deadline. That includes income records and bank statements, expense receipts, contracts, mileage logs and professional registration documents. Digital records are fine and are in any case the norm under MTD, but keep them backed up. Thin records are a common trigger for HMRC enquiries.

When to get specialist help

Consider a specialist medical accountant if you have several income sources and a mix of PAYE and self-employed work, significant expenses or equipment purchases, IR35 uncertainty across contracts, a previous HMRC enquiry, or you are weighing up a personal service company. A medical-sector accountant understands locum filing, the NHS pension interaction and the MTD transition, and can keep you compliant while claiming everything you are entitled to. Our specialist services are built for medical professionals. You can also get in touch to discuss your filing position.

After you have filed

HMRC issues a tax calculation showing what is due. Pay it by 31 January to avoid interest and late-payment penalties, and keep the return and payment confirmation. HMRC can open an enquiry within twelve months of submission; this does not imply a problem, and tidy records make any enquiry straightforward. Then start the next year well by keeping records as you go, which is exactly what MTD now expects.