If you start to do more and/or regular sessions for a practice, there will come a time when HMRC will not accept that you are freelance and will suggest that you are employed by the practice. This can happen when you are not standing in for a missing doctor, but are just an extra pair of hands, or where the practice names you on their website or practice publications as being part of the practice, or where patients start to treat you as ‘their’ doctor.
There used to be a pensions rule whereby you were deemed employed after a specific period, but this does not apply now. However, pensions will need to follow the tax treatment.
If you become employed ‘accidentally’ in the above situation, you would pay PAYE tax on the income and suffer NIC as an employee (with the practice paying employer’s contributions), so would likely end up with less after deductions than if you were still self employed on that source (but not always – as it would depend on your overall income position). From a pension point of view 100% would be pensionable rather than 90% as a locum.