Medical.Accountants
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Tax guides

HMRC Tax Enquiry Help for Doctors

What to do when HMRC opens an enquiry. Expert UK guide for doctors under HMRC enquiry from ICAEW-regulated accountants. Updated for 2026/27.

What should I do if HMRC opens an enquiry?

It depends on your circumstances. Our team reviews your income, structure and records and confirms the right approach for hmrc tax enquiry help for doctors in writing as part of your fixed-fee service.

Fixed fees, specialist healthcare accountants, and every HMRC and NHS Pensions deadline handled.

  • Fixed monthly fee — no surprises
  • Specialist in NHS pension and healthcare tax
  • Onboarding within 48 hours
Get my fixed-fee quoteBook a free 15-min tax review
  • ICAEW & ACCA regulated
  • 5,000+ clients served by ACCOTAX
  • Specialist healthcare accountants

Reviewed by Waqas Sagar ACA FCCA FMAAT, Founder of ACCOTAX, 18+ years' experience · Last reviewed: 8 October 2026 · Updated for the 2026/27 tax year

Medical.Accountants by ACCOTAX, ICAEW/ACCA-regulated chartered accountants, London, serving clients across the UK. Over 5,000 clients served.

Key takeaways

  • The Self Assessment online deadline is 31 January after the end of the tax year, which is also when any balance and the first payment on account are due.
  • Allowable costs include HMRC-approved professional registrations and subscriptions, indemnity where you pay it, business mileage between workplaces and equipment used for work.

Free guide: The Doctor's Tax & NHS Pension Handbook 2026/27

Get the free guide

Which accountancy support fits your income?

Start with how you are paid. Different income sources can need different accounts, returns and expense checks.

How you workWhat we checkSupport to explore
Employed or umbrella (PAYE)Tax codes, eligible employment expenses and whether a tax return is needed.Healthcare tax refund support
Genuinely self-employedBusiness income and expenses, Self Assessment and MTD eligibility.Healthcare Self Assessment service
Your own limited companyCompany accounts, Corporation Tax, director income and off-payroll status where relevant.Healthcare limited company accounts
PartnershipPractice accounts, allocated profit and each partner’s personal tax position.Healthcare partnership accounts

Sound familiar?

Problems we fix for salaried and resident doctors

  • "I think I'm paying too much tax because of a wrong tax code."
  • "I've never claimed my GMC, BMA or royal college fees."
  • "My extra shifts and bank work are taxed wrongly."
  • "I don't know whether I need to file a tax return."
  • "I've received a pension annual allowance letter."

What it's costing you

Leaving it unfixed is rarely free

Overpaid tax
Unclaimed expenses and wrong tax codes mean paying more than you owe, year after year.
HMRC penalties and interest
Late returns attract automatic penalties, plus interest on tax paid late.
Lost evenings
Hours spent on forms, invoices and spreadsheets after a long shift.

General examples — your position depends on your own figures.

How we solve it

What we actually do for you

Refund claims

We claim back overpaid tax for up to four previous years.

Tax code checks

We check every employment and fix wrong codes with HMRC.

Self Assessment

Filed for you when you need one, and explained when you don't.

Pension statement review

We explain your annual allowance position in plain English.

How we help

01

Accounts and tax returns

Year-end accounts and Self Assessment or company returns for hmrc tax enquiry help for doctors, filed on time.

02

Fixed-fee advice through the year

Questions answered by your named accountant, without the clock running.

03

Making Tax Digital

Compatible software set up and quarterly updates filed where MTD applies.

04

NHS pension tax

Annual allowance and taper calculations, with Scheme Pays guidance where a charge arises.

What to know before you decide

Enquiry types

This is one of the questions we work through with hmrc tax enquiry help for doctors at the start of every engagement. We look at your real income, contracts and records, set out the options in plain English and confirm the work and fee in writing.

HMRC Enquiries, Penalties & Late Returns for Doctors & Healthcare Professionals

Information requests

This is one of the questions we work through with hmrc tax enquiry help for doctors at the start of every engagement. We look at your real income, contracts and records, set out the options in plain English and confirm the work and fee in writing.

Penalties

The Self Assessment online deadline is 31 January after the end of the tax year, which is also when any balance and the first payment on account are due. A second payment on account is due on 31 July. Late filing starts with a £100 penalty.

HMRC Enquiries, Penalties & Late Returns for Doctors & Healthcare Professionals

Fee protection insurance

Allowable costs include HMRC-approved professional registrations and subscriptions, indemnity where you pay it, business mileage between workplaces and equipment used for work. Ordinary commuting and personal costs are not allowable. Employees claim through HMRC; the self-employed deduct costs in their accounts.

Your questions answered

Can I appeal an HMRC penalty?

You can appeal a penalty if you have a reasonable excuse for the failure that led to it. Appeals must usually be made within 30 days of the penalty notice date. Common penalties include the £100 charge for late Self Assessment filing. You must provide evidence to support your claim that the delay was beyond your control.

Check the official guidance · www.gov.uk

Help with this question: HMRC Enquiries, Penalties & Late Returns for Doctors & Healthcare Professionals

Want us to check this for you? Get a free review →

What is a reasonable excuse for late filing?

A reasonable excuse is something unexpected or outside your control that stopped you from meeting a tax obligation. Examples include a serious illness, a recent bereavement, or unforeseen postal delays. HMRC evaluates each case based on individual circumstances. You must file the return as soon as the excuse no longer applies to minimize further penalties.

Check the official guidance · www.gov.ukWant us to check this for you? Get a free review →

Should I have tax investigation fee protection insurance?

Tax investigation insurance covers the professional fees incurred during an HMRC enquiry. HMRC can select any taxpayer for a random or targeted check of their records. The costs of defending an enquiry can be substantial, even if no extra tax is found to be due. Many professionals choose this for peace of mind and financial protection.

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What happens if I cannot pay my tax bill on time?

Failing to pay your tax bill on time can result in interest charges and potential surcharges from HMRC. It is important to communicate with HMRC as soon as possible to discuss payment options. A £100 late filing penalty applies if the Self Assessment return is not submitted by 31 January. We assist clients in managing their tax deadlines.

Want us to check this for you? Get a free review →

When is the Self Assessment deadline?

Many hmrc tax enquiry help for doctors must file a Self Assessment return: you need one if you have untaxed income such as private, locum or self-employed work. A high PAYE salary alone does not require Self Assessment for 2026/27; check HMRC's current criteria and any notice to file. The online filing and payment deadline is 31 January after the tax year ends. Under the non-MTD rules, late filing normally triggers an initial £100 penalty, with further penalties for longer delays. A different regime applies from the tax year you join MTD for Income Tax.

Check the official guidance · www.gov.uk

Help with this question: Self Assessment Tax Returns for Doctors & Healthcare Professionals

Want us to check this for you? Get a free review →

What are the penalties for a late tax return?

Many hmrc tax enquiry help for doctors must file a Self Assessment return: you need one if you have untaxed income such as private, locum or self-employed work. A high PAYE salary alone does not require Self Assessment for 2026/27; check HMRC's current criteria and any notice to file. The online filing and payment deadline is 31 January after the tax year ends. Under the non-MTD rules, late filing normally triggers an initial £100 penalty, with further penalties for longer delays. A different regime applies from the tax year you join MTD for Income Tax.

Check the official guidance · www.gov.ukCheck the official guidance · www.gov.uk

Help with this question: Self Assessment Tax Returns for Doctors & Healthcare Professionals

Help with this question: HMRC Enquiries, Penalties & Late Returns for Doctors & Healthcare Professionals

Want us to check this for you? Get a free review →

What are payments on account and when are they due?

Payments on account are two annual payments towards your tax bill if your self-employed liability exceeds a specific threshold. The first payment is due by 31 January and the second by 31 July. Each installment is normally half of the tax due for the prior year. Missing these deadlines can lead to interest charges from HMRC.

Check the official guidance · www.gov.uk

Help with this question: Self Assessment Tax Returns for Doctors & Healthcare Professionals

Want us to check this for you? Get a free review →

How far back can HMRC investigate?

You can claim back overpaid tax relief for up to four previous tax years. For 2026/27 that means claims can still reach back to 2022/23 until 5 April 2027. Employees can claim professional fees online with HMRC, or through Self Assessment if they already file.

Want us to check this for you? Get a free review →

Can I set up a payment plan with HMRC?

HMRC may allow you to set up a Time to Pay arrangement if you are unable to pay your tax in full. This plan allows you to clear your debt through instalments over a set period. You should request this before the payment deadline to minimize penalties. Medical.Accountants can provide the necessary financial figures to support your application.

Want us to check this for you? Get a free review →

What is HMRC's Time to Pay arrangement?

A Time to Pay arrangement allows you to pay your tax debt in manageable instalments over a set period. You must contact HMRC to negotiate this before or shortly after the payment deadline passes. Interest is still charged on the outstanding balance during the arrangement. Approval depends on your ability to prove that you cannot pay in full immediately.

Help with this question: HMRC Enquiries, Penalties & Late Returns for Doctors & Healthcare Professionals

Want us to check this for you? Get a free review →

Can a penalty be appealed?

HMRC penalties can be appealed if there is a valid reason for the non-compliance. You must generally lodge an appeal within thirty days of the penalty notice date. Success often depends on providing clear evidence to support your case. We can assist in communicating with HMRC to resolve these disputes.

Check the official guidance · www.gov.uk

Help with this question: HMRC Enquiries, Penalties & Late Returns for Doctors & Healthcare Professionals

Want us to check this for you? Get a free review →

What is a reasonable excuse?

A reasonable excuse is something unexpected or outside your control that stopped you from meeting a tax obligation. Examples might include serious illness, bereavement, or unforeseen postal delays. HMRC evaluates each case based on whether a person took reasonable care. Simple forgetfulness is typically not accepted as a valid excuse.

Want us to check this for you? Get a free review →

Can I agree a payment plan with HMRC?

HMRC may allow you to settle tax liabilities through a Time to Pay arrangement. These plans are generally negotiated based on your specific financial circumstances and ability to pay. It is important to contact HMRC as soon as you realise you cannot pay in full. We can help you propose realistic payment schedules.

Want us to check this for you? Get a free review →

Quick quote

See what you could save — get a fixed fee in one working day

Three fields. No obligation. A specialist replies, not a sales team.

Packages for your working life

Accountancy packages for doctors

Self-employed income, a limited company, PAYE or a mixture: start with the support that matches how you actually work. We check your status and agree the scope and fee before starting.

Self-employed accountants for doctors packages

For genuine sole-trader income. We prepare your business accounts and Self Assessment, review allowable expenses and explain payments on account.

  • Sole-trader accounts and personal tax return
  • Allowable business expenses reviewed
  • Tax reserve and payment deadline guidance
  • MTD support scoped separately where required

Fixed fee quoted after a review

Discuss this package

Limited company accountants for doctors packages

For clinicians working through their own company. Choose Essential/Compliance, Core/Complete or Growth according to your accounts, bookkeeping and payroll needs.

  • Statutory accounts and Corporation Tax return
  • One director return for salary and dividends from the same company
  • Confirmation statement support; filing fee extra
  • Bookkeeping, VAT and payroll according to your chosen plan

Company packages from £45.83 + VAT / month

Compare company packages

Personal tax return packages for doctors

For employed clinicians, partners and people with mixed income who need a return. We check whether Self Assessment is required and reconcile the relevant income, expenses and pension tax information.

  • Self Assessment requirement checked
  • PAYE and other income reconciled
  • Eligible employment expenses reviewed
  • Pension tax work agreed separately where needed

Fixed fee quoted after a review

Discuss this package

Employment status is determined by the facts, not the package you choose. PAYE, umbrella and partnership arrangements may also apply. A limited company does not override IR35 or off-payroll rules, and not every employed clinician needs a tax return.

Overpaid tax?

Tax refund support for doctors

We review tax codes, eligible professional expenses and overpaid tax, then prepare a claim where you qualify. A refund is not guaranteed; HMRC decides the claim.

£249 + VAT

For refunds up to £5,000, our fee is £249 plus VAT. For refunds above £5,000, add 5% of only the amount above £5,000 to the £249 fee. VAT applies to the total professional fee.

Example: a £6,000 refund means £249 + £50 = £299 plus VAT.

Professional fee, excluding VAT

£249

Ask about a tax refund

This illustrates the fee only, not whether you qualify or how much HMRC will refund. We agree the claim scope and payment terms before work starts.

What's included

Limited company packages — compare what's included

Essential/Compliance

For locums, salaried GPs and dentists with a limited company

from £45.83 + VAT /month

  • FRS 105 or FRS 102 1A statutory accounts
  • Corporation tax return (CT600) and tax computation
  • Confirmation statement preparation and filing support
  • One director Self Assessment return
  • Deadline reminders ahead of every filing date

Core/Complete

For private practice, consultants and associate dentists

from £62.50 + VAT /month

  • Everything in Essential/Compliance
  • Monthly bookkeeping and bank reconciliation
  • Quarterly Making Tax Digital VAT returns
  • Director payroll with RTI filing and pension submissions
  • Quarterly review call on numbers and tax position

Growth

For clinics, dental practices and growing medical teams

from £75.00 + VAT /month

  • Everything in Core/Complete
  • Payroll for up to five employees

Prices exclude VAT. Making Tax Digital quarterly updates available as an add-on. Compare fees

Why clinicians trust us

Chartered accountants who know the NHS

  • ACCOTAX has served over 5,000 clients.
  • Regulated chartered accountants (ICAEW and ACCA).
  • Founded by Waqas Sagar ACA FCCA FMAAT, with 18+ years' experience.

Reviewed by Waqas Sagar ACA FCCA FMAAT

Chartered accountant and founder of ACCOTAX. Last reviewed October 2026.

Get my fixed-fee quote

How it works

  1. 01

    Free call

    A 15-minute chat about your income, structure and deadlines.

  2. 02

    Onboarding in 48 hours

    We set up your records, software and HMRC agent access.

  3. 03

    We handle the rest

    HMRC, NHS Pensions and every deadline, with reminders before each one.

Free resource

Get the doctor expenses checklist free

Tell us where to send it and we'll email it to you.

Your questions, answered

What should I do if HMRC opens an enquiry?
It depends on your circumstances. Our team reviews your income, structure and records and confirms the right approach for hmrc tax enquiry help for doctors in writing as part of your fixed-fee service.
How long does an HMRC enquiry take?
It depends on your circumstances. Our team reviews your income, structure and records and confirms the right approach for hmrc tax enquiry help for doctors in writing as part of your fixed-fee service.
How much does an accountant for doctors under HMRC enquiry cost?
Our packages for hmrc tax enquiry help for doctors start at £45.83 + VAT a month, with Core at £62.50 and Growth at £75 + VAT. The right package depends on your income sources, whether you trade through a company and any payroll, VAT or pension work. We confirm the exact fee in writing before any work begins, so there are no surprise invoices.
Do doctors under HMRC enquiry need to comply with Making Tax Digital?
Making Tax Digital for Income Tax applies from 6 April 2026 to sole traders and landlords whose qualifying income (gross self-employment plus property income) is over £50,000, falling to £30,000 from April 2027 and £20,000 from April 2028. PAYE salary does not count. Hmrc tax enquiry help for doctors trading through a limited company or a partnership are not brought in yet. We set up compatible software and file the quarterly updates for you.
How do I switch to Medical.Accountants?
Switching takes minutes on your side. You sign our engagement letter, we contact your previous accountant for professional clearance and records, and we take over HMRC and Companies House authorisations. You can switch mid-year; we pick up from the last filed return.

Speak to a specialist today

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Book a free 15-min tax review

Related healthcare expertise

Self Assessment Tax Returns for Doctors & Healthcare ProfessionalsHMRC Enquiries, Penalties & Late Returns for Doctors & Healthcare ProfessionalsAccountants for doctors and GPs in the UKLocum doctor accountants: tax, IR35 and NHS pensions
Accountants for healthcare professionalsHealthcare tax questions answered

General information for the 2026/27 tax year, prepared from the official guidance linked below. It is not personalised tax or regulated financial advice. Rules and circumstances can change; confirm your position before acting.

Official sources referred to on this page: HMRC compliance checks factsheets; HMRC penalties and appeals (GOV.UK); HMRC Time to Pay; HMRC Self Assessment deadlines and penalties (GOV.UK).

Official guidance

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