For a taxable stipend--subject to FIT but not Soc Sec/Med, simply reporting the income on Schedule C with a corresponding equal amount reported on the Schedule C as an expense does NOT work, because for FIT purposes that reduces the income to zero. 

So, in my son's case, he just graduated from college as undergrad (and thus would get a 1098-T), but this Fall, he is a graduate PhD student with a stipend.  Thus, in the responses above, particularly the one that said to select "no" if he got a 1098-T, well, he did get a 1098-T as an undergrad for the tuition he paid undergrad.  He is now a PhD student at a different school with a stipend.  So, three questions:

1.  How will he declare his income on turbotax as a stipend?

2.  Does anyone have a ballpark about how much, percentage-wise, he should pay in quarterly tax payments?  The reason is that part of his stipend may be offset by educational expenses, depending on which form the university uses at the end of the year (1099-misc or 1098-T). So the percentage might be lower than it would be for ordinary income. He's single with no dependents.

3.  Does anyone know if PhD stipends are taxable in the state of Pennsylvania for state or local taxes?

Thanks in advance.

I am having the same problem and I am also a student. I got a stipend amount for my internship but it came in a 1099-NEC form, how do I go about entering this in?

If you are performing any duties in conjunction with the stipend (e.g. teaching assistant, research assistant, student teacher, clerical work, etc.), then the payment is considered "self-employment income". This income is subject to both income tax and self-employment taxes 

To enter your 1099-NEC, you may use this shortcut in TurboTax to get to the right page: 

1. Open your return.
2. Search for 1099-NEC with the magnifying glass tool at the top of the page.
3. Click on the Jump to 1099-NEC link at the top of the search results. 
4. Click Add a 1099-NEC.
5. Enter the information as shown on your form. 
6. Follow the on-screen instructions. 
7. On the page titled Guess what? You can deduct expenses for the example work choose Yes, I have expenses to deduct.
8. On the page titled Self-employed 1099-NEC Income select the Schedule C you are inputting this income for. If this is a new Schedule C for this year, you can add a new business on this screen.

To confirm your 1099-NEC was linked to your Schedule C, please follow the instructions below:

1. Open your return.
2. Search for Sch C with the magnifying glass tool at the top of the page.
3. Click on the Jump to Sch C link at the top of the search results. 
4. On the page titled Your 2020 self-employed work summary, you should see your 1099-NEC listed with the corresponding amount. 
5. Click review next to the income from your 1099-NEC. 
6. Follow the on-screen instructions on the following pages. 

I got a 1099-NEC for a stipend that was NOT wages or in exchange for any services.  I understand that it is subject to income tax, but if reported as a 1099 NEC, then it will treat it as subject to social security and medicare tax as well.  The provider will not correct it.  How do I report this properly?

You can enter the stipend as Miscellaneous Income using these steps:

1. Click on Federal > Wages & Income   
2. In the Less Common Income section , click on the Start/Update box next to Miscellaneous Income, 1099-A, 1099-COn the Miscellaneous Income screen, click on the Start/Revisit box next to Other reportable income. 
3. On the Any Other Taxable Income? screen, click the Yes box.
4. Add the income and description on the next screen, Other Taxable Income.
5. This amount will appear on line 8 of the 1040 (Other Income from Schedule 1).

@dblasband

What do I do about the  improperly issued 1099 NEC, then?  Just ignore it?  Won't this be a red flag?

You can enter the income as ordinary income. This could be a red flag to the IRS and you may hear from them in the next year. You should be prepared to defend your position that this income was not wages.

Here is an article that discusses stipend income in detail.