The final refund or balance due amount shown on your Federal Form 1040 has already taken into account any self-employment (SE) tax that you might owe. The SE tax is not paid separately.
You can see this when you take a look at your Form 1040. Line 24 shows your total tax, which will include SE tax reported as part of line 23. Then, the total tax will be compared to line 33 which shows your total payments (including any refundable credits). If the total payments is greater than your total tax, then you will have a refund.
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