I'd like to share some information about running an annual payroll in QuickBooks Online.
QuickBooks Online Payroll currently supports weekly, bi-weekly, semi-monthly, and monthly pay schedules. You can check out this link for more information about setting up and managing payroll schedules: Set up and manage payroll schedules.
As a workaround, you can create and add Bonus payroll item for your employee and use it as a pay type.
Like this:
Go to Payroll, then Employees.
Click on the employee's name, hit the pencil icon next to Pay.
Under How much do you pay?, click the pencil icon next to Additional pay types.
Under Common pay types, put a check mark on the Bonus box.
Select Save.
Once done, go back to the Employees page and click the Run payroll button.
Select the pay schedule and click Continue.
Put a check mark the employee's name and click the amount under Salary. Select the option Skip salary this time only.