The self-employment tax is calculated along with everything else that is on your tax return. It is not a separate payment. When all of your calculations are done, if you have tax due it will be on line 37, which you can pay in a variety of ways. If you are getting a refund it will be on line 35a.
If you have federal tax due you can pay by mailing your payment with the 1040V voucher, (which has the address printed on it, having the payment taken out of a designated bank account, or you can pay directly on the IRS website.
https://www.irs.gov/payments/direct-pay
https://ttlc.intuit.com/community/tax-payments/help/how-can-i-pay-my-federal-taxes/00/26212
https://ttlc.intuit.com/community/tax-payments/help/how-do-i-pay-my-irs-tax-due-with-a-check-or-mone...
You must pay your state tax due using the state’s preferred method of receiving payment. For most states that will be by making a payment to the state’s own tax website, or by mailing a check or money order.
https://ttlc.intuit.com/questions/1900884-what-are-my-options-for-getting-my-state-refund-or-for-pay...
https://ttlc.intuit.com/questions/1901670-how-do-i-contact-my-state-department-of-revenue
To apply for a payment plan with the IRS
Apply Online for a Payment Plan
**Disclaimer: Every effort has been made to offer the most correct information possible. The poster disclaims any legal responsibility for the accuracy of the information that is contained in this post.**
