Sometimes you may wish to run an annual scheme. This is common with single director-only companies where the employee or director is only paid once a year. However, if you want to run an annual scheme, and there are no weekly or monthly pay runs, you must ensure you have registered the scheme with HMRC as annual.
HMRC say the following:
If you pay your employees only once a year, and all in the same tax month, you can register with HMRC as an ‘annual scheme’.
This means you send reports and make payments to HMRC annually. If you pay your employees on different days in the same tax month, you need to send an FPS on or before each payday. You do not need to send an Employer Payment Summary (EPS) for the months when you do not pay your employees.
To register, contact the employer helpline and tell them which month you pay your employees. You’ll need your 13-character Accounts Office reference number - this is on the letter HMRC sent you when you registered as an employer.
HMRC is sending estimated charges
If you receive estimated charges when no submissions have been made, it could be because you aren't registered for an annual scheme. HMRC automated system has been set to receive 1 submission per PAYE scheme during each tax month and if nothing is received, estimated charges and late filing fees may be issued.
For any tax periods that HMRC expect a submission, you can create an EPS to try and wipe those fines in the meantime.
Past tax periods: No payment EPS
Future tax periods: Period of inactivity EPS