Hi there, Mariz. Unfortunately, there is no direct option to set up an annual pay schedule in QuickBooks Online Payroll, which only supports the four default pay frequencies: weekly, biweekly, semimonthly, and monthly. However, as a work around, you can utilize running a bonus cheque separately from your regular paycheque to run a one-time annual payroll.
Bonus Paycheques enable you to process one-time payments while ensuring accurate tax calculations, compliance, and proper recordkeeping. This method allows you to handle annual payments without affecting your existing pay schedules or making permanent changes to your payroll system, providing a practical solution for your needs.
Here’s how you can do this:
- Go to the Payroll menu, then select Employees.
- Click the Run payroll drop-down arrow and choose Bonus only.

- On the Run Payroll: Bonus Only page, select one of the following options:
- As net pay — Take-home pay or what's left AFTER payroll withholdings are taken out.
- As gross pay — Total pay or what you make BEFORE payroll withholdings and applicable deductions are taken out.
- Select Continue.
- Enter the Pay date and choose the employee to include in this bonus run.
- Enter the bonus amount for each employee.
- (Optional) Enter a message to appear in the Memo box of the cheque or pay stub.
- (Optional) Select Edit next to Payroll options, check the options you want, and select Apply. Payroll options include only options relevant to this bonus run.
- Select Preview payroll and review the details.
- Select Submit payroll.
- (Optional) Select Print cheques or Print pay stubs. (The cheques or pay stubs open in a separate page.)
- Once your payroll is all set, select Finish payroll.
By doing the steps above, you can now process your one-time annual payroll without disrupting your regular payroll schedules. Let us know if you need any further assistance, we're here to assist you.