How to pay an employee

3 minute read


First register your employee via the Employees page. See our guide for more details.

Next head over to the Pay tab, your current in progress pay run should be at the top of the page. Click on it and the payment page for that pay period will open.

You should see a list of employees you have already paid on the left-hand side. If you have not paid anyone yet this will be empty. Add your new employee by clicking the ‘Add Employee’ button on the right. You can start to type your employees name to find them or just click the down arrow on the employee box to select them from a list of eligible employees.

Add Employee to Pay Run

For an employee to be eligible to be paid in a pay run they must have a tax code and their start date must be on or before the payment date for the pay run. You can go back to the employee page and edit your employee if you have made a mistake.

If you want to pay this employee every future pay run, make sure the ‘Pay this employee every pay run’ box is checked. If you are on our free plan this option will not be available to you.

Click Add to add the employee.


You may need to add your employee into a pension plan at this stage. Click the small action menu button on the employee payment and select Pension Plan. Use an effective date before the pay run date and select the pension from the drop-down list.


You can now add the payments and deductions you need to make to the employee. Use the ‘Add Payment’ button on the right to open the Add Payment dialog.

Select the payment type you want, for example ‘Hours’, change the description if you don’t like the default and add in the amounts. If this payment should be made every month, e.g. Salary then the ‘Regular Payment’ box should be checked. If this is a one off payment e.g. Bonus then uncheck this box.

Add Payment Hours

If you select one of the Statutory Payment types then the figures will be used when calculating your payment report and when submitting RTI to HMRC. It is important to select the correct statutory payment type or you may not be able to claim relief against your NI bill for those payments.

All named payment types are submit to Tax, NICs and subject to Pensions. If you need to make another type of payment, e.g. an expenses reimbursement or a mileage claim then select the Other payment type. You can then select if the payment will be taxed, NICed or included in pension calculations. Please refer to HMRC guidelines for the type of payment you are making.

Add Payment Other

The amount of tax, NICs and pension will be calculated automatically when you save a payment or deduction.


If you need to add additional deductions you can do this from the ‘Add Deduction’ button. Select a Deduction from Net if the employee should pay tax before the deduction is made, e.g. for a Deduction of Earnings Order. Select Deduction from Gross if tax should not be charged e.g. to cover a shortfall in a till. If you need to do something else select the ‘Other’ option and check the boxes as appropriate.

All Done

Everything is saved as you go along so there is nothing left to do.

Just issue your employee a payslip when you complete the pay run.