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[edited April 13, 2016]
If you are on a J-1 visa, you will be exempt from the Substantial Presence Test for the first 2 (if non-student) or 5 (if student) calendar years that you are in the US. This means that you are considered a non-resident aliens for US tax purposes.
You will need to file a Form 1040NR to report your US source income. TurboTax does not support Form 1040NR. You may want to try https://www.sprintax.com/ which is specifically designed to help international student nonresident aliens with their US tax returns.
If you are in the US beyond this exempt period, you will file as a US resident.
Click this link for more information from the IRS on US Tax Guide for Aliens
You can enter your stipend as a scholarship on your US income tax return. You would also be able to claim a treaty exemption to this income if one applies.
You would include your stipend income under the education section and if applicable, you will enter the amount of the treaty exemption as a negative amount under other miscellaneous income. You may also need to attach Form 8833 to your tax return. (Attaching this form will require that you mail in your return. You will need to select - file by mail under the file tab.)
Since Form 8833 is not supported by TurboTax, here is the link to the IRS website regarding claiming a tax treaty benefit:
https://www.irs.gov/Individuals/International-Taxpayers/Claiming-Tax-Treaty-Benefits
To enter your stipend as a scholarship into TurboTax:
If a treaty exemption applies, you will now need to enter a negative amount for the treaty exemption under other miscellaneous income
To enter your treaty exemption under as other miscellaneous income:
You would enter your stipend as a scholarship in the education section (credits and deductions). You need to click through all the irrelevant questions until you get to enter the scholarship.
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