If you are the shareholder of an S Corporation, you may be confused about the correct way to report health insurance premiums paid on your behalf. You can slog through this publication from the IRS website: S Corporation Compensation and Medical Insurance Issues.
Or, you can go straight to the bottom line:
Health insurance premiums paid by an S Corporation on behalf of its greater than 2% shareholder-employees are deductible by the S Corporation. This is true whether the S Corp pays the premium directly or reimburses the shareholder-employee for the premiums. As of 2016, any type of health insurance plan qualifies. Newly popular medical sharing ministries (like Medi Share) are not eligible, but the Medicare supplement deducted from a shareholder’s Social Security check is. (The tricky part is figuring out how much it is, since you get your statement at around the same time your W2 must be filed.)
The amount paid (whether directly or as reimbursement) must be included in Box 1 and Box 14 of the shareholder-employee’s W2. This means that the health insurance premium will be considered wages subject to income tax, but NOT subject to Social Security, Medicare, or FUTA.
Usually, the amount reported in Box 14 (included as taxable wages in Box 1) is then deducted on the shareholder’s personal tax return, making it a “wash” on the personal tax return. The net result is that the S Corporation gets a deduction, thus reducing its taxable income.