Query Regarding Self Assessment and National Insurance (NI) Payments

I would like to clarify whether Self Assessment payments include both tax and National Insurance (NI). I recently discovered that NI contributions should be included as part of the Self Assessment process. As a sole trader, I may have misunderstood the process. I mistakenly registered as an employer under PAYE, created a Business Tax Account, and ran payroll to “pay myself” through PAYE—subsequently paying NI via this route. Given this situation, have I effectively paid National Insurance twice?

Not HMRC...you need to speak to HMRC and cancel and close down your PAYE scheme immediately. You CANNOT operate PAYE via self employment to pay yourself, it is effectively "fraudulent"...claiming deductions against profit that are not due! You are assessed on your trading profit, PAYE payments to yourself are NOT allowable deductions from profit, your figures will be all over the place. You must cancel all PAYE transactions to date and get HMRC to refund tax/ni paid over and account for it under self assessment. Profit assessable to tax from your business will calculate class 4 ni automatically each year, class 1 is NOT payable. Class 2 would also be due (but treated as paid unless profit too low in which case you tick the box to pay voluntarilyif you wish to do so). Given all of the above I would strongly recommend you make an appointment with a local accountant to sort this out, as it is a very complicated "mess".

Thank You! I will follow your suggestion.

Hi Benny Lui,
As you have paid the NI under PAYE, you should not be declaring the income as self employment on your tax return.
If you have, you will have been paying it twice and will need to amend it.
Thank you. 

HMRC...you are missing the point, the questioner has paid Tax/NI by operating PAYE against his own self employment, this is not allowable/possible, as a sole trader he is the business, the business is him, an individual cannot employ themselves where there is no ltd company and it is the PAYE situation that needs to be addressed and closed down not making an adjustment to self employment.