Why not use a general accountant for my pharmacy?

You can, but pharmacy income does not behave like ordinary retail. NHS reimbursement, the fee per item and the medicine margin have to be reconciled, and the VAT split between zero-rated dispensing and standard-rated retail has to be right. Accountants who do not see it often miss it.

Can you reconcile NHS reimbursement to my accounts?

Yes. We take your dispensing schedules and reconcile the Drug Tariff reimbursement, the Single Activity Fee and the margin to what reached your bank, so the accounts reflect earned income rather than a cash total.

Can I be in the NHS Pension Scheme as a pharmacy owner?

Community pharmacy contractors cannot join the NHS Pension Scheme for their pharmacy income, unlike GP and dental contractors. Some employed pharmacists can. We factor that into how we structure owner pay and pension.

Community Pharmacy Accounts

Written and reviewed by the Pharmacy Accountants editorial team. Last reviewed 28 July 2026.

We prepare the year-end accounts for community pharmacy owners and reconcile the part that general accountants get wrong: the NHS side. Your income is not a till total. It is Drug Tariff reimbursement, fees and margin arriving on a schedule, and the accounts have to reflect that.

This is the annual accounts and the tax return that follows them, done by people who read a pharmacy for a living. If you want to understand where the money comes from first, our guide to how community pharmacy funding works explains the model; here we keep your books straight against it.

What Your Year-End Accounts Include

We produce your statutory or sole trader accounts, the Corporation Tax or Self Assessment return that goes with them, and a reconciliation of NHS income to what actually landed. In England that means reimbursement at Drug Tariff prices plus the Single Activity Fee of £1.46 per item from 1 April 2025, set against the funding the contract delivers.

We separate your dispensing income from retail so the accounts show the real margin on each, and we track the medicine margin the contract builds in. Scotland and Wales fund differently, and we apply the right framework rather than default to the England figures.

Where the Dispensing and Retail Split Gets Awkward

VAT is the awkward part. Dispensed NHS prescription drugs are zero-rated at 0%, while over the counter and retail sales are standard-rated at 20%. Your pharmacy makes a mixed supply, and the split has to be right or you overpay or underpay. Our page on VAT for pharmacies covers the mechanics; in the accounts we make the numbers agree.

The margin is the other trap. Reimbursement does not match what you paid the wholesaler, so gross profit on the NHS side is a calculation, not a figure off an invoice. We build it properly instead of treating dispensing like ordinary retail.

How We Reconcile the Month

We take your dispensing schedules, wholesaler statements and till data and reconcile them to the bank. That is how a pharmacy's real position appears, since the cash and the earned income sit in different months. You get accounts that a lender or a buyer will accept without argument.

We keep the bookkeeping current through the year rather than reconstruct it at the deadline. Regular reconciliation means fewer surprises at year end and a set of figures you can manage the business on.

What Pharmacy Accounts Cost

We charge a fixed fee agreed before we start. It is set for the year, so you can budget it, and it does not move because dispensing volume rose or a reconciliation ran long.

The fee depends on the size of the pharmacy, the number of transactions and whether you trade as a company or a sole trader. A single branch costs less than a small group. We quote against your actual scale, not a headline rate.