If you are a doctor, GP or hospital consultant with any income outside straightforward NHS PAYE, you almost certainly fall inside Self Assessment. This guide explains who has to file, how to register, the deadlines that matter for the 2026/27 tax year, how payments on account work, what National Insurance you owe, and how Making Tax Digital for Income Tax changes things from April 2026.

It is general information rather than personal advice. We are a specialist medical accounting firm, so where a point is specific to GP partners, locums or consultants we flag it, and we link to the deeper role-specific guides at the end.

Who Has to File a Self Assessment Return?

The simple test is whether you have income that has not already been fully taxed at source. NHS salary paid through PAYE is taxed at source. Most other medical income is not, so it has to be declared through a return. Your working structure decides which pages of the return you complete:

  • GP partners are self-employed. The partnership files an SA800 partnership return, and each partner's share of profit flows onto the partnership pages (SA104) of their personal return. A partner is taxed on their profit share, not their drawings, which is one of the most common things people get wrong in their first year.
  • Freelance GP locums are usually sole traders, declaring their locum income on the self-employment pages (SA103). A locum who instead trades through a personal service company has the company file corporation tax, but still completes a personal return for any salary and dividends taken.
  • Salaried GPs are employees taxed under PAYE. They only need to file if they have extra income on top, for example occasional locum sessions, private work or expert-witness fees.
  • Hospital consultants are NHS employees on PAYE, but most have private work (insurance medicals, medico-legal reports, self-pay clinics) that is self-employed or company income and must be declared.

You also need to file, whatever your structure, if any of these apply for the year:

  • your total income is over £100,000;
  • you (or your partner) have to pay the High Income Child Benefit Charge;
  • you have an NHS pension annual allowance charge to report (common for higher-earning consultants and GP partners, see our annual allowance and tapered allowance guides below);
  • you have untaxed income from property, savings, dividends or capital gains above the relevant thresholds.

A salaried GP or consultant with only their NHS PAYE income and nothing on the side generally does not need a return at all.

How to Register for Self Assessment

If 2026/27 is your first year with income that needs a return (you became a GP partner, started locum work, or took on private practice), you must tell HMRC by 5 October 2027. Register as a sole trader, as a partner, or for a partnership, depending on your role. HMRC then issues your Unique Taxpayer Reference (UTR) and enrols you for online filing.

Registering late does not automatically mean a penalty if you still pay on time, but leaving it until January is risky because the UTR and online access can take a couple of weeks to arrive. New GP partners should also make sure the partnership itself is registered and has its own UTR, as the SA800 cannot be filed without it.

Self Assessment Deadlines for 2026/27

The 2026/27 tax year runs from 6 April 2026 to 5 April 2027. The deadlines that follow it are:

  • 5 October 2027: tell HMRC you need to file, if you are new to Self Assessment.
  • 31 October 2027: deadline for paper returns.
  • 31 January 2028: deadline for online returns and for paying any balancing payment for 2026/27.
  • 31 July: the second payment on account instalment, where payments on account apply (see below).

The online deadline is the one almost everyone uses. Miss it and HMRC charges an automatic £100 penalty even if you owe no tax, with daily penalties and interest building from there. Specialist medical accountants tend to ask for records in late summer or early autumn, well before the January crush, partly because the January deadline overlaps with the busiest clinical period of the year.

Payments on Account: Why Your First Bill Feels Huge

Self-employed doctors are usually caught by payments on account, which are advance instalments towards the following year's tax. They apply where your Self Assessment liability is more than £1,000 and less than 80% of your tax was collected at source.

When they apply, you make two interim payments of 50% each of the prior year's liability, due on 31 January and 31 July. The catch hits in your first self-employed year. On 31 January you can be asked for the balancing payment for the year just ended plus the first 50% instalment towards the next year, so the cash demand can look like roughly 150% of a normal year's tax in one go. This is timing, not extra tax, but it surprises a lot of new GP partners and locums.

If your income has genuinely fallen (you reduced sessions, left a partnership, or had a one-off spike the year before), you can apply to reduce your payments on account. Reduce them too far and HMRC charges interest on the shortfall, so this is worth getting right rather than guessing. Setting money aside as you earn, ideally in a separate tax account, is the single most useful habit for a self-employed doctor.

National Insurance on Self-Employed Medical Income (2026/27)

GP partners and freelance locums pay Class 4 National Insurance through Self Assessment alongside income tax:

  • 6% on profits between £12,570 and £50,270;
  • 2% on profits above £50,270.

The Class 4 main rate fell from 9% to 6% from 6 April 2024, so older guides quoting 9% are out of date. Class 2 National Insurance is no longer a required weekly payment from 6 April 2024 either: if your profits are at or above the small profits threshold, you are treated as having paid Class 2 and keep your state pension entitlement, with no separate weekly charge to budget for. Doctors with profits below that level can still pay voluntary Class 2 to protect their record if they choose.

What You Can Claim, and How NHS Pension Charges Appear

Self-employed doctors deduct expenses incurred wholly and exclusively for the profession. Common allowable items include your GMC retention fee and relevant Royal College or specialty subscriptions, medical indemnity (MDU, MPS or MDDUS) for private and non-clinical work, genuine CPD, accountancy fees, and business mileage between sites. The HMRC approved mileage rate for cars 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 after that. Home-to-first-site travel is ordinary commuting and is not deductible. Our full expenses guide and the locum-specific list are linked below.

One medical point that often surfaces on the return is the NHS pension annual allowance charge. The annual allowance is £60,000 for 2025/26, tapering for very high earners, and it is measured on the growth in your pension (the pension input amount), not the contributions you pay. If your input amount exceeds your available allowance, the excess is taxed at your marginal rate and reported on your Self Assessment return. Where the charge is large enough you may be able to ask the NHS scheme to settle it under Scheme Pays rather than paying it personally. These are specialist calculations, covered in the annual allowance and Scheme Pays guides below.

Making Tax Digital for Income Tax from April 2026

The biggest change to Self Assessment in years is Making Tax Digital for Income Tax (MTD for ITSA), which replaces the annual paper-style process with digital records and quarterly updates for those in scope. It is phased in by qualifying income (your gross trading plus property income, tested on the relevant prior year's return):

  • £50,000 and above: from 6 April 2026;
  • £30,000 and above: from 6 April 2027;
  • £20,000 and above: from 6 April 2028.

The old £10,000 threshold that circulated for years has been dropped, so ignore any guide still quoting it. For doctors, the practical effect is:

  • Most full-time GP locums and unincorporated private GPs exceed £50,000 and are in scope from 6 April 2026, so they will need MTD-compatible software, digital records and quarterly submissions.
  • Limited companies are out of MTD for ITSA (it is income tax, not corporation tax), so a locum trading through a personal service company is not brought in by their company income.
  • General partnerships are deferred with no confirmed start date, so a GP partnership is not yet mandated at partnership level. A partner's own qualifying income from sole-trader private work can still bring their personal position into MTD.
  • Salaried GPs and consultants are not pulled in by employment income alone, but private earnings on top (locum sessions, expert-witness work, media) can take you over the threshold.

If you are likely to be caught from April 2026, the time to move onto compliant software and clean digital records is now, not the week before your first quarterly update is due.

Getting Your Records Ready

Whether you file yourself or use a specialist, the return is only as good as the records behind it. Gather these well before the deadline:

  • P60s and P45s for any NHS or other employment;
  • your partnership profit allocation (SA800 figures) if you are a GP partner;
  • locum income records and any agency or PCSE statements;
  • private practice and expert-witness income;
  • bank statements and receipts evidencing professional expenses;
  • NHS pension statements and any annual allowance pension savings statement;
  • details of property, savings, dividend or capital gains income.

A specialist medical accountant adds value mainly where the position is genuinely medical: getting the partnership profit allocation onto the right pages, handling the NHS pension annual allowance charge and Scheme Pays, deciding whether private work belongs in a company, and keeping a locum's IR35 position straight. For a fully PAYE doctor with no extra income, a return may not even be needed.

If your return involves multiple income streams, a partnership profit share, or an NHS pension allowance charge, professional support often pays for itself in tax saved and penalties avoided. Get in touch to talk through your situation with a specialist medical accountant.