A community pharmacy carries a real payroll: dispensers, counter staff, and often a second pharmacist or locum cover. Employer (Class 1 secondary) NIC is 15% above a £5,000 secondary threshold from 6 April 2025, and the Employment Allowance is £10,500 from the same date for eligible employers. A lot of live accounting content and payroll software documentation still quotes the old 13.8% rate above a £9,100 threshold with a £5,000 allowance, all of which are stale. Running payroll on stale figures either overpays HMRC or creates a compliance liability. We run your pharmacy payroll on current rates, model the true cost of your workforce, and apply the Employment Allowance correctly where you are eligible.
From 6 April 2025, employer (Class 1 secondary) NIC is charged at 15% on earnings above a £5,000 secondary threshold per employee per year. The previous rate of 13.8% above a £9,100 threshold is stale and should not be used. Across a dispenser and counter-staff payroll, the difference between the old and current rate is material. Payroll run on stale figures creates a PAYE compliance exposure.
The Employment Allowance rose to £10,500 from 6 April 2025, offsetting employer secondary NIC for eligible employers. The former £5,000 cap is stale. The allowance offsets the 15% employer NIC charge, which is particularly valuable for a pharmacy with a small-to-medium team. However, eligibility conditions still apply, including the single-director-only bar, so it is not automatic for every pharmacy structure.
Adding a dispenser or changing a part-time contract changes the employer NIC cost in ways that are not immediately obvious from the gross wage alone. The true on-cost of a hire includes the 15% employer NIC above £5,000, pension auto-enrolment contributions, and any impact on the Employment Allowance headroom. Planning workforce changes without modelling the full cost is a common source of budget error.
Pharmacies with eligible staff must comply with workplace pension auto-enrolment. Where staff have NHS employment history or have previously worked in an NHS-linked role, there may also be NHS Pension Scheme mechanics to navigate. Payroll that handles the RTI submissions correctly but gets the pension obligations wrong creates a different compliance risk.
We run your pharmacy payroll using the current employer NIC rate of 15% above the £5,000 secondary threshold, apply the Employment Allowance correctly where you are eligible, and submit RTI to HMRC on time. We do not run stale-figure payroll. If your current provider is using 13.8% or a £9,100 threshold, we will flag it and correct it.
We model the true employer on-cost of your current team and any planned changes, including the 15% NIC above £5,000, pension auto-enrolment contributions, and the Employment Allowance offset. Where you are considering a hire, a rota change, or a shift from employed to locum cover, we show the cost difference before you commit. To estimate your employer NIC position, speak to us and we will work through the numbers.
We manage your auto-enrolment obligations alongside payroll, including assessing which staff are eligible, setting up the pension provider relationship, and handling re-enrolment cycles. Where NHS Pension Scheme questions arise, we advise on the accounting and payroll mechanics within our scope and coordinate with specialist pension advisers where the professional position requires it.
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