If you are a S-Corp owner, you will need to first establish the Sep with the IRS under your company's name. Please read this IRS link carefully on how to set up the SEP with the IRS. This must be done before you start making contributions for yourself or other shareholders.
Then when you prepare your 1120S return in Turbo Tax Business, you will prepare it in Federal Taxes>deductions>compensation and benefits>Retirement plans contributions. Here you will enter shareholder contributions.
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