If PAYE is not calculating when you run a pay run and you are migrating your payroll from another system, you should check the employee opening balances are set. This article will assist you in ensuring that the opening balances are set correctly. You can find the year to date figures on their most recent payslip for your current payroll platform.
If the employee opening balances are not set and you are using a cumulative tax code, the system will think the employee is being paid for the first time in the tax year as the system has no previous earnings recorded for the employee. This means your employee will be receiving the tax free pay threshold amount up to that point in the tax year.
If your employee is a new employee and doesn't have a P45 you will need to complete this form to determine the tax code depending on what they choose in the employee statement section and enter that on the Tax and NI details page.