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The stipend is only "Non Taxable" in your employer's imagination. The stipend is additional pay, the same as if you got a raise of $50 a month. It is taxable income. All payments from your employer are supposed to be included on your W-2. You don't have to debate this with your employer or ask for a corrected W-2. You can just report it correctly on your tax return, in spite of the employer's error.
To report the bonus on your tax return, you enter the income as additional wages that were not reported on a W-2. You will pay income tax on it, and also the Social Security and Medicare taxes that the employer should have withheld. You will pay the same amount that you would have paid if your employer had handled it correctly and included the stipend in your W-2.
The stipend will be reported on Form 1040 line 1g. Form 8919 will be included in your return, with reason code H in column (c). Form 8919 calculates the Social Security and Medicare taxes. The total of these taxes will appear on Schedule 2 line 6 and will be included in your total tax liability.
Here's how to enter the stipend in TurboTax.
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