It is a matter for individual employers as to whether they wish to pay the EU Settlement Scheme fee on behalf of an employee.
In terms of employers choosing to reimburse their staff for the cost of applying to the settlement scheme, taxation rules are not a matter for the Home Office. However, HMRC has advised that in situations like these, where an employer pays or reimburses their employees’ application costs, such a payment would be taxable as earnings from their employment and may also attract a National Insurance contributions (NICs) charge. However, employers can also choose to meet the cost of this tax and NICs charge for their employees. For many employers this can be managed within their existing arrangements with HMRC, using a PAYE Settlement Agreement (PSA) which allows employers to make one annual payment to cover all the tax and NICs due on minor, irregular or impracticable expenses or benefits for their staff.