Accountants for doctors, GPs and locums

What does a GP accountant need for partnership accounts and tax returns?

Each partner pays Income Tax and Class 4 National Insurance on their share of the practice profit, so the partnership accounts and the profit split come first.

The nominated partner sends the partnership tax return (form SA800) for 2025/26 by 31 October 2026 on paper or 31 January 2027 online. Each partner reports their share on the partnership pages (SA104) of their own return, online by 31 January 2027.

A practice year ending on any date from 31 March to 4 April can be treated as ending on 5 April. Tax-year reporting has applied since 6 April 2023, and any transition profit from the 2023/24 changeover is spread up to 2027/28, so it may still be on your return.

In England and Wales, GP partners (Type 1 practitioners) then complete an annual certificate of pensionable profits from the finished returns. The 2024/25 certificate was due by 28 February 2026.

Tax for salaried GPs and hospital doctors: is your tax code right?

PAYE takes your tax through your tax code, so the main thing to check is that the code is right. A code ending W1, M1 or X is an emergency code, used when a new employer lacks your previous pay details, for example after a rotation.

A second post usually has a BR code (taxed at 20%) or D0 (taxed at 40%), and an S prefix means Scottish rates. You can check your codes in your personal tax account or the HMRC app.

You can claim tax relief on the GMC annual fee. You can also claim on subscriptions to HMRC-approved bodies, including the Medical Defence Union, the Medical Protection Society, the Medical and Dental Defence Union of Scotland (MDDUS) and the Royal College of General Practitioners. BMA relief is limited to 85% of the subscription.

For business travel in your own car (not ordinary commuting), HMRC's approved rate from 6 April 2026 is 55p a mile for the first 10,000 business miles, then 25p. If your employer pays less, you can claim relief on the difference.

Salaried GPs in England and Wales also complete a Type 2 self-assessment form each year. This is an NHS Pensions form, separate from your HMRC tax return.

How do locum doctors pay tax and NHS pension contributions?

Self-employed locums pay Income Tax and Class 4 National Insurance through Self Assessment. Class 4 is 6% on profits between £12,570 and £50,270, and 2% above that. If you have not filed before, register by 5 October after your first tax year ends (5 October 2027 if you started in 2026/27).

Once your bill reaches £1,000, you usually also make payments on account (two advance payments towards next year's bill). For 2026/27 they are due on 31 January 2027 and 31 July 2027, unless more than 80% of your tax was already paid, for example through your tax code. Our payments on account calculator shows what you will pay on each date.

Freelance GP locums in England and Wales send a Form A for each invoice and a Form B each month. Both employee and employer contributions must reach NHS England through Primary Care Support England (PCSE), or your local health board in Wales, by the 7th of the following month.

Forms must be received within 10 weeks of the work ending, or that work cannot be pensioned. Pensionable income is 90% of the fee excluding the employer element (14.38% of pensionable pay for 2026/27).

Private practice: sole trader or limited company?

Sole trader profits are taxed with your other income at 20%, 40% and 45% (Scottish rates go up to 48%), plus Class 4 National Insurance.

A company pays Corporation Tax at 19% on profits up to £50,000 and 25% over £250,000, with a sliding rate in between (marginal relief). Dividends are then taxed at 10.75%, 35.75% or 39.35% above a £500 allowance.

For a GP locum, one factor can decide it: fees invoiced through a limited company cannot go on Form A, so that work cannot be pensioned as freelance locum work.

Medical care by a registered doctor is exempt from VAT when its main purpose is protecting, maintaining or restoring the patient's health. Medico-legal work for the courts, pre-employment medicals and purely cosmetic work are standard-rated and count towards the £90,000 VAT registration threshold. Medicals for insurance companies can fall either side, so check section 4.8 of VAT Notice 701/57.

HCA can help with company formation, accounts, Corporation Tax and VAT returns.

How does the NHS pension annual allowance work in 2026/27?

The annual allowance is the pension saving you can build up in a tax year before a tax charge applies. It is £60,000 for 2026/27, unchanged since 6 April 2023. For the NHS scheme it measures the increase in your benefits (the pension input amount), not what you paid in.

The allowance gets smaller (tapers) only if both income tests are met. Threshold income (broadly your income after your own pension contributions) must be over £200,000, and adjusted income (income plus pension savings, including your employer's share) over £260,000. It then falls by £1 for every £2 over £260,000, to a minimum of £10,000.

This year's allowance is used first, then unused allowance from the previous 3 tax years, earliest year first. You can only carry forward from years you were in a registered pension scheme.

NHS Pensions sends a pension savings statement by 6 October if your growth in the 1995/2008 or 2015 Scheme is over £60,000 and it had your membership details by 6 July. It has said some 2024/25 statements are delayed, with no confirmed issue date. If you expect to be near the allowance and have no statement, ask NHS Pensions for one rather than assuming you are under it.

Any charge is taxed at your own rates on your Self Assessment return. Through Scheme Pays, NHS Pensions pays it for you in return for a permanent cut to your pension that includes interest.

NHS Pensions must do this (mandatory Scheme Pays) if the charge is over £2,000 and your growth in one NHS scheme is over £60,000. The election, on form SPE2, cannot be revoked and must arrive by 31 July 2027 for a 2025/26 charge, or 31 July 2028 for 2026/27. If you plan to retire before then, send it before you retire.

After retirement, NHS Pensions only considers it under voluntary Scheme Pays. That route also covers charges caused by a tapered allowance or by combined growth across both NHS schemes, with no £2,000 minimum. You then remain liable for the charge, and for any interest if HMRC is paid after 31 January.

From 1 October 2023, the McCloud remedy moved service from 1 April 2015 to 31 March 2022 back into the 1995/2008 Scheme for affected members, who choose 1995/2008 or 2015 Scheme benefits for that period. This may change their annual allowance position for 2015/16 to 2021/22.

Scotland and Northern Ireland have separate NHS schemes, run by the Scottish Public Pensions Agency and the HSC Pension Service. The annual allowance rules are UK-wide.

Worked example: a GP partner over the annual allowance

Dr Amira Khan is hypothetical. She is a GP partner in England with income of £150,000 in 2026/27, so her threshold income is under £200,000 and her allowance stays at £60,000.

Her pension savings statement shows growth of £75,000 in the 2015 Scheme, £15,000 over the allowance. Carry forward covers £10,000 (nothing unused from 2023/24, £4,000 from 2024/25 and £6,000 from 2025/26), leaving £5,000 taxable.

Her income is above £125,140, so the £5,000 is taxed at 45%: a charge of £2,250, reported on her 2026/27 return by 31 January 2028.

The charge is over £2,000 and her growth is over £60,000, so NHS Pensions must pay it if her SPE2 arrives by 31 July 2028 and before she retires. If she were a Scottish taxpayer, the rate would be 48%, a charge of £2,400.

When does Making Tax Digital for Income Tax start for doctors?

Making Tax Digital for Income Tax means digital records and quarterly updates to HMRC through software. It has applied since 6 April 2026, with two later start dates confirmed.

Qualifying income is self-employment and property income before expenses. PAYE salary does not count, and nor does a GP partner's share of partnership profit; HMRC says partnerships will join later, with no date set.

So a locum with £35,000 of fees in 2025/26 starts on 6 April 2027, while a salaried doctor with no other income is not affected. Quarterly updates are due on 7 August, 7 November, 7 February and 7 May.

Common questions

Your next step

Check your next Self Assessment filing and payment dates on our tax calendar. Then call 0113 460 1786 or email ask@hca-accountants.com and tell us which of these you are: GP partner, salaried doctor, locum or private practice.

Related pages

• Self Assessment tax returns
• Accounts preparation
• Payroll processing
• Tax calendar
• Payments on account calculator
• Contact HCA
• Do I need Making Tax Digital for Income Tax?
• Tax rates for 2026/27