How to Set Up a PAYE Scheme for Your UK Business

How to Set Up a PAYE Scheme for Your UK Business Hero Image

Get 50% off our services for the first 6 months when you sign up to one of our Pre-Built or Bespoke Packages!

If your UK business is hiring employees or paying yourself as a director, you’re legally required to set up a PAYE (Pay As You Earn) scheme. PAYE allows HMRC to collect Income Tax and National Insurance contributions (NICs) directly from employee wages.

In this guide, we’ll take you through the step-by-step process of setting up a PAYE scheme for your business, ensuring you meet your legal obligations while managing payroll efficiently.

What Is PAYE and Why Is It Important?

PAYE (Pay As You Earn) is HMRC’s system for collecting Income Tax and National Insurance Contributions (NICs) directly from an employee’s salary before they receive their wages. It ensures that taxes are deducted at the source, helping both employees and the government maintain a smooth and efficient tax process.

If you employ staff or pay yourself as a director of a limited company, setting up a PAYE scheme is a legal requirement in most cases. You must operate PAYE if any of the following conditions apply:

  • An employee earns more than £123 per week (£533 per month or £6,396 per year).
  • You are paying salaries to directors of a limited company.
  • Employees receive expenses and benefits (e.g., company cars, health insurance, bonuses).

Without a PAYE scheme, businesses cannot legally process payroll for their employees, leading to potential penalties from HMRC. Setting up a PAYE scheme correctly ensures that tax and NICs are deducted accurately, avoiding compliance issues.

For full guidance, visit HMRC’s PAYE for employers page.

Step 1: Register as an Employer with HMRC

Before you can set up a PAYE scheme, you must register as an employer with HMRC. This applies even if you are the only employee (e.g., a sole director of a limited company paying yourself a salary).

When to Register

You should register at least four weeks before your first payday to allow HMRC time to process your application. However, you cannot register more than two months before you start paying employees.

How to Register

  1. Visit the official HMRC Employer Registration page.
  2. Provide details about your business, including:
    • The legal structure (sole trader, partnership, or limited company).
    • Your business name and address.
    • The date you will start paying employees.
    • Your company’s Unique Taxpayer Reference (UTR) (if applicable).

What You’ll Receive After Registering

Once your registration is complete, HMRC will issue:

  • Employer PAYE Reference Number – This is used to identify your business when submitting payroll information.
  • Accounts Office Reference Number – This is required for making PAYE payments to HMRC.

These reference numbers are essential for managing payroll, filing Real-Time Information (RTI) returns, and ensuring compliance with PAYE regulations.

Step 2: Choose Payroll Software

To efficiently set up a PAYE scheme, you’ll need payroll software to calculate employee wages, tax deductions, and submit Real-Time Information (RTI) reports to HMRC. Choosing the right software ensures accuracy, compliance, and efficiency in managing payroll.

Key Features to Look For

When selecting payroll software, consider:

  • HMRC-Recognised Software – Ensure your chosen software is compatible with HMRC’s RTI system. Check the full list of approved software here.
  • Automatic Tax Calculations – The software should handle Income Tax, National Insurance Contributions (NICs), and student loan repayments.
  • Payslip Generation – Easily create and distribute digital or printed payslips for employees.
  • RTI Submission to HMRC – The software must allow you to submit payroll reports (FPS & EPS) directly to HMRC, as required by PAYE regulations.
  • Pension Auto-Enrolment Support – If you employ staff, your software should help with automatic pension enrolment to stay compliant with workplace pension laws.

Popular Payroll Software Options

Free Payroll Software (For Small Employers)

  • HMRC Basic PAYE Tools – A simple, free tool for businesses with fewer than 10 employees. However, it lacks features like payslip generation and automation.

Paid Payroll Software (For Growing Businesses)

  • Xero Payroll – Ideal for small and medium-sized businesses, with automation and integration with accounting software.
  • QuickBooks Payroll – A user-friendly option that syncs payroll with your financial records.
  • Sage Payroll – Comprehensive payroll management with pension auto-enrolment features.
  • BrightPay – A cost-effective solution for businesses needing easy payroll processing and RTI compliance.

Choosing the right payroll software is crucial for streamlining your PAYE scheme, ensuring compliance with HMRC, and reducing administrative burden.

Step 3: Collect Employee Details

To correctly set up a PAYE scheme, you must collect key details from each employee before running payroll. This ensures that Income Tax and National Insurance Contributions (NICs) are calculated accurately.

Essential Employee Information to Collect

  • Full Name and Address – Ensures proper identification and accurate record-keeping.
  • National Insurance (NI) Number – Required for reporting tax and NI contributions to HMRC.
  • Employment Start Date – Helps determine tax codes and payroll processing.
  • Bank Details – If paying wages via bank transfer, collect the employee’s account number and sort code.
  • Right to Work Documentation – If hiring a new employee, you must check their right to work in the UK. You can do this via the GOV.UK Right to Work checker.

Tax Information: P45 or Starter Checklist

You need to determine the correct tax code for each employee. To do this, request one of the following:

  • P45 Form – If the employee has worked elsewhere in the same tax year, they should provide a P45 from their previous employer. This form shows their earnings and tax details so far.
  • Starter Checklist – If they don’t have a P45, they must complete HMRC’s Starter Checklist. This form helps you apply the correct tax code and avoid emergency tax deductions.

Collecting and verifying these details is an essential step in registering employees for PAYE and ensuring smooth payroll processing.

Complete payroll services for your business

 Payroll (PAYE) Services

Get 50% off our services for the first 6 months when you sign up to one of our Pre-Built or Bespoke Packages!

Speak to an accounting expert

If you’re unsure what level of support you need, our friendly team are on hand to help you pick the right package for you.

Step 4: Calculate Deductions and Run Payroll

Once your PAYE scheme is set up and your employees are registered in your payroll system, you can begin processing payroll. This involves calculating tax deductions, generating payslips, and submitting reports to HMRC.

1. Calculate Payroll Deductions

Your payroll software will automatically calculate deductions from an employee’s gross pay.

These include:

  • Income Tax – Based on the employee’s tax code and earnings. Use HMRC’s tax calculator here.
  • National Insurance Contributions (NICs) – Includes both:
  • Employee NICs (deducted from wages).
  • Employer NICs (paid separately by the business).
  • Student Loan Repayments – If applicable, repayments are deducted based on the employee’s loan plan type. Check repayment thresholds here.
  • Pension Contributions – If your business operates auto-enrolment, employee and employer pension contributions will also be deducted.

2. Generate Payslips

You must provide each employee with a payslip detailing their:

  • Gross Pay – Total earnings before deductions.
  • Deductions – A breakdown of Income Tax, NICs, pensions, and any other adjustments.
  • Net Pay – The final amount paid to the employee.

Payslips can be digital or paper-based, but they must be issued on or before payday.

3. Submit RTI Reports to HMRC

Under Real-Time Information (RTI) rules, you must report payroll details to HMRC every payday. The main submission is the:

Full Payment Submission (FPS) – Sent to HMRC on or before each payday, showing:

  • Employee earnings.
  • Tax and NICs deducted.
  • Student loan and pension contributions (if applicable).

Employer Payment Summary (EPS) – If needed, this is used to reclaim statutory payments (e.g., sick pay, maternity pay) or notify HMRC of no payments in a period.

You can file RTI reports directly through your payroll software, ensuring compliance with PAYE regulations.

For full RTI guidance, visit HMRC’s RTI reporting page.

Step 5: Pay HMRC

After deducting Income Tax, National Insurance Contributions (NICs), and other payroll liabilities, you must pay these amounts to HMRC on time to avoid penalties.

How to Pay HMRC

Once you’ve submitted your RTI Full Payment Submission (FPS), your payroll software will calculate the total PAYE tax and NICs owed for the period. You can pay HMRC using:

  • Online Banking (Faster Payments, CHAPS, or Bacs) – The fastest and most secure method.
  • Direct Debit – Set up an automated payment through HMRC’s Direct Debit service.
  • Debit/Credit Card – Payments can be made via the HMRC payment portal.
  • Cheque or Bank Transfer – Only an option for businesses that cannot pay electronically.

PAYE Payment Deadlines

To remain compliant with PAYE regulations, ensure your payments reach HMRC by:

  • 22nd of each month – If paying electronically (e.g., bank transfer, Direct Debit).
  • 19th of each month – If paying by cheque or other non-electronic methods.

If you pay late, HMRC may charge interest and penalties. Check the latest penalty structure here.

Step 6: Maintain Payroll Records

Keeping accurate payroll records is a legal requirement for PAYE compliance and helps in case of HMRC audits.

What Records Should You Keep?

Employers must store payroll records for at least three years and ensure they include:

  • Employee details – Names, NI numbers, and tax codes.
  • Payslips and payroll reports – Gross pay, deductions, and net pay.
  • RTI Submissions – Copies of FPS and EPS reports sent to HMRC.
  • PAYE payments to HMRC – Proof of tax and NIC payments made.
  • Statutory payments – Records of sick pay, maternity pay, or redundancy payments.

Failing to maintain accurate payroll records can result in HMRC penalties of up to £3,000. For full record-keeping guidelines, visit HMRC’s payroll record-keeping page.

Tips for Managing PAYE Efficiently

Setting up a PAYE scheme is just the first step—ongoing management is key to staying compliant and avoiding penalties. Here are some expert tips to help you run payroll smoothly.

1. Stay Organised with Payroll Software

Using HMRC-recognised payroll software can streamline PAYE processes by:

  • Automating calculations for Income Tax, NICs, and student loan repayments.
  • Tracking important deadlines for PAYE payments and RTI submissions.
  • Generating payslips and keeping digital payroll records to ensure compliance.

Popular options: Xero, QuickBooks, BrightPay.

2. Understand PAYE Deadlines to Avoid Penalties

RTI Full Payment Submission (FPS): Must be sent to HMRC on or before each payday.
PAYE Tax and NIC Payments:

  • Electronic payments – Due by the 22nd of each month.
  • Non-electronic payments – Due by the 19th of each month.

Late payments can result in interest charges and penalties. Learn more about PAYE late penalties here.

3. Consider Outsourcing Payroll to Save Time

If managing payroll in-house becomes overwhelming, outsourcing to a payroll provider or accountant can:

  • Ensure compliance with PAYE, RTI, and auto-enrolment regulations.
  • Reduce administrative workload, freeing up time for core business tasks.
  • Minimise errors and avoid costly mistakes.

If you’re looking for expert payroll management, consider Accounting Wise’s payroll services to handle everything from PAYE registration to RTI submissions.

Conclusion: Setting Up a PAYE Scheme the Right Way

Setting up a PAYE scheme is a crucial step for any UK business that employs staff. By following the steps outlined in this guide—registering with HMRC, choosing payroll software, calculating deductions, and meeting PAYE deadlines—you’ll ensure compliance while managing payroll efficiently.

While running PAYE and payroll can seem complex, the right tools and processes make it easier. Staying organised, understanding key deadlines, and using HMRC-recognised payroll software can help prevent errors and avoid penalties.

At Accounting Wise, we specialise in PAYE registration, payroll management, and tax compliance. Whether you need one-off guidance or a fully managed payroll service, we’re here to help.

Need expert payroll support? Contact us today at Accounting Wise to streamline your payroll process and stay compliant with HMRC regulations.

Complete payroll services for your business

 Payroll (PAYE) Services

Need help setting up PAYE? Talk to Accounting Wise today for expert payroll solutions tailored to your business needs.

Newsletter Subscription - Accounting Wise

Join Our Newsletter!

Get expert accounting tips, tax updates, and business insights straight to your inbox. Sign up today and stay one step ahead!

Newsletter Signup

Hot Topics

More related Accounting Community, News & Resources

Accounting Wise - what is a unique taxpayer reference (UTR)

What Is a Unique Taxpayer Reference (UTR)?

When starting a business or becoming self-employed in the UK, there are plenty of forms and numbers you need to keep track of. One of the most important identifiers you’ll encounter is the Unique Taxpayer Reference (UTR) number.
Accounting Wise - What are the Benefits of Paying Corporation Tax Early

What are the Benefits of Paying Corporation Tax Early?

Discover why UK companies choose to pay corporation tax early. Learn the benefits, HMRC interest rules, and how early payment can support your business.
Accounting Wise - what is national insurance

What is National Insurance?

This National Insurance overview aims to provide a detailed understanding of National Insurance, covering its purpose, the rates at which contributions are calculated, and the impact it has on your entitlement to state benefits and retirement planning.