The employee has not been added to the payroll. The employee has a release date. The employee is marked as inactive. Go to the Payroll Info tab. In the Payroll Schedule drop-down, select the correct Payroll Schedule. Select OK to save the changes. Run your scheduled payroll again to check if the missing employee is already showing. Employee is Missing from your QuickBooks Desktop Payroll When an employee is removed from payroll, any remaining funds that were encumbered for the employer's portion of deductions are released.