Doctors, GPs and consultants need an accountant who understands how the NHS, the NHS Pension Scheme and HMRC interact, not just one who can file a tax return. This overview sets out what specialist medical accounting services cover, how the numbers differ by role, and where to go next for the detail on your exact situation. It is general information, not advice, and the firm works only with medical clients.

Your income may come from several places at once: an NHS contract or salary, GP partnership profits, locum sessions, private clinics and medico-legal work. Each has its own tax rules. A general high-street accountant rarely sees NHS Pension annual allowance work, GMS contract income or the prohibition on selling NHS goodwill, which is exactly where a specialist earns their place.

Why doctors need specialist medical accounting services

Medical finances sit on rules that simply do not arise for most other clients. The same accountant who serves a local trade business will not, day to day, deal with:

  • NHS Pension annual allowance and tapered allowance calculations, where the measure for a defined-benefit scheme is the capitalised growth in your pension (the pension input amount), not the contributions paid in;
  • GP partnership accounts, profit-share allocation and partner buy-in and buy-out via capital accounts;
  • IR35 / off-payroll status for a locum trading through a personal service company (the rules apply, they have not been abolished or repealed);
  • splitting NHS and private income cleanly, including the VAT line between exempt medical care and standard-rated medico-legal or cosmetic work;
  • profession-specific expenses: GMC retention fee, MDU / MPS / MDDUS indemnity, BMA and Royal College subscriptions, and CPD relevant to current practice.

Getting any of these wrong is expensive. An overlooked annual allowance charge, a missed Scheme Pays election or an incorporation that quietly stops your NHS pension accruing can cost far more than a year of fees.

Services for GP partners

GP partners carry the most complex set of requirements, because they combine self-employment, an NHS contract and (often) practice premises. Core work here includes:

Partnership accounts and tax. Preparing accounts that fairly reflect profit shares, capital contributions and drawings, then filing the partnership return (SA800) with each partner's share flowing to their own return. A partner is taxed on profit share, not drawings, and pays Class 4 NIC at 6% on profits from £12,570 to £50,270, then 2% above (2025/26). Class 2 is no longer a required payment for profits at or above the small profits threshold (from 6 April 2024), so no weekly Class 2 charge applies.

NHS contract income. Practice funding comes through the Global Sum (weighted by the Carr-Hill formula), QOF, enhanced services and PCN / Network Contract DES funding (including ARRS), not through any single national per-patient figure. Our guide to how GMS funding works and the QOF income guide cover the mechanics.

NHS Pension certification. A partner is a Type 1 practitioner and completes the Annual Certificate of Pensionable Profits each year via PCSE, so the right tiered contribution is recorded against net NHS-derived profit.

For the full partner picture, including basis-period and entry-exit points, see our GP partnership tax guide and the profit-sharing tax planning guide.

Services for salaried GPs and consultants

Employed doctors are on PAYE for their main role, but rarely have a simple tax position once private work appears. Typical work:

Self assessment across income sources. Bringing together PAYE income with private practice, locum sessions and medico-legal fees, so nothing is missed and reliefs are claimed correctly.

NHS Pension annual allowance. Monitoring pension growth against the £60,000 annual allowance (2025/26) and watching for the tapered allowance, which bites where threshold income exceeds £200,000 and adjusted income exceeds £260,000, reducing the allowance by £1 for every £2 over £260,000 down to a £10,000 floor. Consultants and high-earning GPs are most exposed. Where a charge arises, a Scheme Pays election can settle it; see our Scheme Pays deadlines guide and the annual allowance guide.

A salaried GP weighing up the partnership route can compare the two positions in our GP partner versus salaried GP tax comparison.

Services for locum doctors

Locums need clarity on status before anything else, because it drives how their income is taxed:

Sole trader or personal service company. A sole-trader locum files self assessment (SA103) and has no intermediary, so IR35 does not apply; status is judged on the employed-versus-self-employed factors. A locum working through a personal service company is inside the off-payroll framework: for NHS Trust work the Trust (or the agency as fee-payer) issues the status determination, not the locum. Our locum IR35 guide and limited company pros and cons set out the choice.

Expenses and mileage. Claiming legitimate costs (indemnity for private and non-clinical work, professional fees, equipment via capital allowances, and travel between sites). HMRC's approved mileage rate is 55p per mile for the first 10,000 business miles in 2026/27 (it rose from 45p on 6 April 2026), then 25p; home to first site is non-deductible commuting. See the locum expenses guide.

NHS pension as a locum. Freelance GP locums pension their income via Locum forms A and B through the PCSE / Solo route; see pensioning locum income.

NHS pension and tax planning, joined up

The single most valuable thing a medical accountant does is connect your tax position to your NHS Pension. That means tracking pension input against the £60,000 allowance (2025/26), spotting the taper early, advising on Scheme Pays where a charge arises (a 2025/26 charge must be elected by 31 July 2027), and timing income to reduce the impact of the tapered allowance. The lifetime allowance was abolished from 6 April 2024 and replaced by the Lump Sum Allowance (£268,275) and the Lump Sum and Death Benefit Allowance (£1,073,100), so planning now centres on the annual allowance and lump-sum limits rather than a lifetime cap. The 2023 increase in the standard annual allowance from £40,000 to £60,000 is the historical change behind today's figures.

Incorporation and private work

Doctors regularly ask whether incorporating saves tax. The honest answer for medical clients is "only for private work, and only sometimes". A limited company cannot hold an NHS GMS or PMS contract, and company income and dividends are not NHS-pensionable, so any tax saving has to be set against lost pension accrual. The case has narrowed further because dividend tax rises from 8.75% / 33.75% (2025/26) to 10.75% / 35.75% from 6 April 2026 (additional rate stays 39.35%, with a £500 allowance). The real drivers are usually managing the annual-allowance taper, retained earnings and family planning, not a headline tax cut. We model the saving and the pension loss together; see our GP limited company guide and the incorporation step-by-step guide.

VAT, capital allowances and goodwill: the medical specifics

VAT. Medical care by a registered practitioner is exempt where the principal purpose is the protection, maintenance or restoration of health. Cosmetic-only work and medico-legal or expert-witness reports can be standard-rated. The registration threshold is £90,000 of non-exempt turnover (deregistration £88,000), counting taxable supplies only. See our GP VAT registration guide and the private income guide.

Capital allowances. The Annual Investment Allowance is £1,000,000 (100% relief on qualifying plant and machinery). The main-rate writing-down allowance falls from 18% to 14% from 1 April 2026 (corporation tax) / 6 April 2026 (income tax), with the special-rate pool unchanged at 6%; a new 40% first-year allowance applies to new, unused main-rate plant from 1 January 2026.

Goodwill. A crucial point that catches general accountants out: NHS GP goodwill cannot be sold (prohibited since 1 April 2004, currently under SI 2019/251), so the dental-style "sell your goodwill and claim relief" approach does not apply to an NHS practice. A GP transaction is about tangible assets, premises and capital accounts, plus any private goodwill. Business Asset Disposal Relief applies only to a private-practice disposal and runs at 18% for a disposal on or after 6 April 2026 (it was 14% from 6 April 2025 to 5 April 2026, and 10% before that). The CGT annual exempt amount is £3,000 (2025/26). See whether GP goodwill can be sold and selling a private medical practice.

Compliance, deadlines and Making Tax Digital

Specialist services keep all of your obligations on track: self assessment and partnership filing deadlines, payments on account, and correct expense claims for GMC fees, indemnity, BMA and Royal College subscriptions and CPD. From 6 April 2026, Making Tax Digital for Income Tax begins for sole-trader and landlord income over £50,000 (then £30,000 from April 2027 and £20,000 from April 2028). That catches most full-time locums and unincorporated private GPs. Limited companies are out of MTD for Income Tax, and general partnerships are deferred with no confirmed date. See our self assessment filing guide and GP tax deductions list.

Choosing the right provider

When you compare medical accounting services, look for genuine medical specialisation (real experience with GP partnerships, NHS Pension annual allowance work and locum status), qualified staff, a service range that reaches from compliance to planning, and a proactive approach that flags changes such as the 2026/27 dividend and mileage updates before they cost you. To see how we work, visit our services page or try our tax calculators.

The right medical accounting services provider becomes a long-term partner, adapting their advice as your career moves from salaried post to partnership, private practice or retirement, and as the tax rules change around you.