Payroll Setup Guide: First-Time Employer Checklist
Setting up payroll for the first time involves more moving parts than most new employers expect — registration, software, pensions, and an ongoing cycle of deadlines that starts the moment you pay someone. This guide walks through every step in order, so nothing gets missed before your first payday arrives.
📋 Haven't Registered for PAYE Yet?
This is the essential first step, and it needs to happen before anything else here.
PAYE Registration Guide →The 6 Steps to Running Payroll
- Register as an employer for PAYE with HMRC, ideally 4-6 weeks before your first payday.
- Choose HMRC-recognised payroll software that can submit Real Time Information (RTI) reports.
- Collect starter information from each new employee — a P45 from their previous job, or a starter checklist if they don't have one.
- Set up a workplace pension scheme ready for automatic enrolment duties, which begin from your employee's very first day.
- Run payroll each pay period, calculating pay and deductions, submitting an FPS on or before payday, and paying HMRC by the deadline.
- Handle year-end tasks — issuing P60s and, if relevant, reporting benefits in kind on P11Ds.
Interactive: First Payroll Checklist
Tick off each item as you complete it to track your progress toward your first payroll run.
Payroll Setup Checklist
Choosing Payroll Software
Your payroll software must be able to submit Real Time Information (RTI) to HMRC — this is non-negotiable, not optional, for any UK employer. HMRC publishes a list of recognised commercial software, ranging from free basic options suitable for a handful of employees, through to full-featured paid packages that handle pensions, benefits, and multi-employee scheduling automatically.
For a very small business with one or two employees, HMRC's own free Basic PAYE Tools can be sufficient, though it lacks the automation and pension integration that paid software typically offers. As headcount grows, most businesses move to paid cloud payroll software specifically because it automates pension contribution calculations, payslip generation, and year-end reporting — tasks that become noticeably more time-consuming to do manually once you're managing more than a couple of employees.
Workplace Pension & Auto-Enrolment
Automatic enrolment duties apply from the very first day your first employee starts working for you — there's no grace period for new employers, unlike some other compliance areas. You must assess every employee against three earnings-based categories to determine whether they need to be automatically enrolled, can opt in voluntarily, or fall outside the scheme entirely.
| Category | Earnings threshold (2026/27) | What happens |
|---|---|---|
| Eligible jobholder | Over £10,000/year, aged 22 to State Pension age | Must be automatically enrolled |
| Non-eligible jobholder | £6,240–£10,000/year, or outside the 22-to-State-Pension-age band | Can opt in; employer must contribute if they do |
| Entitled worker | Under £6,240/year | Can ask to join; no employer contribution required |
For eligible jobholders, the minimum total contribution is 8% of qualifying earnings (the band between £6,240 and £50,270 for 2026/27), with at least 3% from the employer and the remainder from the employee, which typically includes basic rate tax relief added automatically. You must also complete a declaration of compliance with The Pensions Regulator within 5 months of your duties start date, confirming you've met your obligations — missing this deadline can result in fines even if you've actually set everything up correctly.
Running Payroll Each Period
Once set up, running payroll becomes a repeating cycle: calculate each employee's gross pay, apply the correct tax code and NI category, deduct Income Tax, National Insurance, pension contributions and any student loan repayments, then generate a payslip showing the breakdown. An FPS (Full Payment Submission) reporting this information must normally be sent to HMRC on or before each payday — not after, which is a common mistake for employers used to other, more retrospective types of reporting.
You then need to pay HMRC the Income Tax, employee NI, and employer NI you've collected, by the 22nd of the following month if paying electronically (or the 19th by post) — monthly for most employers, though very small employers can sometimes arrange to pay quarterly instead.
Payslips, P60s & Year-End
Every employee is legally entitled to an itemised payslip on or before payday, showing gross pay, deductions, and net pay. At the end of the tax year, every employee still working for you on 5 April must receive a P60 by 31 May, summarising their total pay and deductions for the year — an important document for mortgage applications, tax queries, and their own records.
If you've provided any taxable benefits in kind during the year (a company car, private medical insurance, and so on), these need reporting on a P11D for each affected employee, plus a P11D(b) summarising the Class 1A National Insurance due, both due by 6 July following the tax year end.
Record-Keeping
HMRC requires payroll records to be kept for at least 3 years from the end of the tax year they relate to, covering pay, deductions, taxable benefits, and any statutory payments (sick pay, maternity pay, and so on) made to employees. Most payroll software handles this automatically, but it's worth confirming your specific provider's retention policy actually meets this minimum, particularly if you ever switch software or providers partway through a tax year.
👥 Understand the Full Cost of Employer NI
Before running your first payroll, see exactly what employer National Insurance will add to your costs.
Employer NI Explained →Common First-Payroll Mistakes
The single most common mistake is leaving PAYE registration too late, then discovering references haven't arrived in time for the first payday — plan backwards from your intended start date, not forwards from when you happen to get round to registering. A close second is misapplying tax codes for new starters without a P45, either guessing at a code or failing to use the correct emergency tax code and starter declaration, which can leave an employee overtaxed for months before it's corrected.
On the pensions side, many new employers mistakenly believe there's a grace period before auto-enrolment duties kick in, or that a very small business is somehow exempt — neither is true. Duties start from day one regardless of company size, and the declaration of compliance deadline (5 months from your duties start date) catches out employers who assume simply setting up a pension scheme is enough without also formally declaring compliance to The Pensions Regulator.
Finally, underestimating the true cost of a new hire is a frequent planning mistake — employer National Insurance, minimum pension contributions, and Employers' Liability insurance can add well over 20% on top of gross salary, a figure that's easy to overlook when budgeting for a first hire based on salary alone.