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Late PAYE Registration: Can You Run Payroll Before Your PAYE Reference Arrives?

A practical UK guide for limited-company owners on what to do if the first payday is close but the employer PAYE reference has not arrived yet.

Your first payday is close, your employee is expecting to be paid, and HMRC still has not sent your employer PAYE reference. That situation creates panic because owners assume payroll must stop until the letter arrives.

It does not.

HMRC's own guidance says you must register as an employer before the first payday, but it also explains what to do if you need to pay someone before the reference arrives: run payroll, store the Full Payment Submission (FPS), and send a late FPS once you have the PAYE reference.

This guide is practical payroll guidance for UK limited-company owners. It is not tax, legal, or accountancy advice. If you have already missed a payday, have paid cash informally, or are unsure whether someone should have been treated as an employee at all, get advice before you repeat the mistake.

Quick answer

If your PAYE reference has not arrived and payday is due:

Make sure you have actually applied to register as an employer.
Run payroll on time using the correct gross pay, deductions, and employee details.
Store the FPS in your payroll software if the software supports that workflow.
Send the FPS to HMRC as soon as your reference arrives, even if it is then late.
Keep clear records showing when you registered, when payday happened, what you paid, and when the FPS was finally sent.

The main risk is not that HMRC forbids the payment. The main risk is paying people informally, skipping payroll records, or assuming you can "sort it out later" without a clean audit trail.

What HMRC expects before the first payday

GOV.UK says you must register as an employer before the first payday, and you cannot register more than 2 months before you start paying people.

That timing catches many new owner-managers out because the PAYE reference is sent by letter, not instantly. In practice, that means:

register as soon as your first pay date is real, not when you are "thinking about hiring";
allow time for the reference to arrive;
avoid promising a first payday that leaves no admin margin at all.

If the first payday is imminent, the key question becomes whether you registered in time and can evidence that. If you did, you move into late-submission handling rather than unregistered-employer chaos.

Can you still pay the employee?

Yes, if the employee should be paid, do not assume the answer is to delay wages until HMRC posts the reference.

HMRC's registration guidance explicitly says that if you need to pay an employee before you get your employer PAYE reference number, you should:

run payroll;
store your FPS;
send a late FPS to HMRC.

That is the practical answer most owners need. The payment itself is not the problem. The problem is failing to process it through payroll properly.

Step by step: what to do when the reference has not arrived

1. Confirm that employer registration has actually been submitted

Do not build your plan around "I thought my accountant did it" or "I filled in something online last week".

Confirm:

the date the employer registration was submitted;
the legal employer name;
the expected first payday entered in the registration;
who is responsible for watching for the PAYE and Accounts Office references.

If you have not registered at all yet, fix that immediately. Do not wait until after payday to start the registration process.

2. Run payroll for the real payday

Use your payroll software to calculate pay and deductions as normal. That means keeping the usual records:

employee name, address, date of birth, and National Insurance number if available;
tax code information if available;
gross pay;
tax and National Insurance deductions;
pension deductions if applicable;
net pay;
payment date.

The goal is that when the PAYE reference arrives, you are not rebuilding payroll from bank transfers and memory.

3. Store the FPS

HMRC's guidance is to store the FPS first if you do not yet have the employer PAYE reference. Many payroll systems have a stored or held submission workflow for this situation.

If your software cannot do that cleanly, do not guess. Check the software provider's documentation before payday.

4. Submit the late FPS once the reference arrives

As soon as the employer PAYE reference is available, send the FPS. Do not wait until the next regular pay run if the late submission can be filed earlier.

HMRC's general RTI rule is that an FPS should be sent on or before payday unless an exception applies. In this case the practical point is to complete the delayed filing promptly and keep a note of why it was late.

5. Keep a written note on the payroll file

For a first-payroll delay, keep a short internal note covering:

first payday date;
date employer registration was submitted;
date PAYE reference arrived;
date FPS was sent;
who reviewed the late-filing reason.

That note matters if HMRC later asks why the first FPS was late or if the employee questions why their payroll setup took longer than expected.

What not to do

These are the mistakes that make a manageable delay look much worse:

paying wages in cash or by transfer with no payroll calculation behind them;
issuing a handwritten or improvised payslip and planning to "properly payroll it next month";
changing the payday after the fact purely to avoid late RTI questions;
forgetting that pension, right to work, and employment-record duties still exist even if the PAYE reference is delayed;
assuming no FPS is needed because it is the first employee.

Worked example

Greenway Interiors Ltd hires its first employee with a payday of Friday 27 June 2026.

The director submitted employer registration on 16 June 2026. By 27 June, the PAYE reference still has not arrived.

The compliant route is:

Greenway runs payroll dated 27 June 2026;
the software stores the FPS rather than sending it immediately;
the employee is paid the correct net amount on 27 June;
the PAYE reference arrives the following week;
Greenway sends the late FPS straight away and keeps a note that the first payroll was run before the reference arrived.

The non-compliant route would have been paying the employee from online banking with no payroll record and trying to fold it into July.

Common mistakes

Registering too late: many owners wait until the person starts work, not until the first payday is planned.
Treating the first payment as informal: HMRC still expects payroll records and RTI handling.
Forgetting other first-employer duties: PAYE registration is only one part of becoming an employer.
No evidence trail: if HMRC asks later, "we were waiting for a letter" is much weaker than a dated audit note and stored payroll reports.

When this becomes a bigger problem

Escalate the issue if any of these are true:

you paid more than one payroll without proper RTI submissions;
the person should have been enrolled or assessed for a workplace pension and that has also been missed;
the employee has been paid irregularly without payslips or records;
the first worker may not actually have been self-employed.

At that point, you are not dealing with a simple first-reference delay anymore. You are dealing with a wider payroll compliance cleanup.

Keep the first payroll from turning into a pattern

One late setup is recoverable. Repeated payroll admin drift is what creates bigger HMRC and employee problems.

Workmax helps small employers keep employee records, approvals, timesheets, payroll calculations, RTI submissions, and audit notes in one workflow, so the first pay run is not rebuilt from inboxes and bank exports.

If you are about to hire or have just hired, pair this with the 2026/27 UK payroll calendar, the new employer compliance checklist, and a clear first-payday workflow.

Book a payroll demo