If you were self employed you would need to deduct the SEP-IRA contribution on your 1040. But as an s-corp owner you don't do that because it has already been deducted on the 1120-s and used to calculate the k-1 box 1. This is a good explanation. See the very end. https://www.upcounsel.com/sep-ira-for-s-corp
a little more detail:
K-1 (1120-S) box 13 is for credits. A SEP-IRA contribution is a deduction not a credit. See https://www.irs.gov/pub/irs-pdf/i1120ssk.pdf page 17-18 for info on Box 13.
On the 1120-S, line 17 is subtracted from the LLC (taxed as an S-Corp)'s income (along with other deductions) to arrive at line 21 ordinary business income/loss. Each owner's share of line 21 is reported on their K-1 box 1.
So as you can see the SEP is reported on a K-1 line. It is already been used to reduce the business's income. You should not put it on your 1040.
Does that make sense?
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