Most contractors who used to work in the NHS have been informed more than 2 years ago that they fall within IR35 and they need to be paid through payroll.
There are other workers who have taken the risk to continue getting paid through their limited companies. This decision is not wise and may lead to inquiries being opened by HMRC in the future.
The risky decision however can still comply with IR35 Regulations but only on few instances e.g;
*You declare all the payments from the NHS work on your payroll
* You have been disputing your employment status and following the proper channels to get it rectified
The correct way of proceeding if you have been assessed to be within IR35 is to go on payroll. The agency should take you onto their own payroll preferably to avoid falling into tax avoidance schemes with some payment intermediaries.