IRS instruction for box 3 says it either goes as other income (line 21 of schedule 1) or on Schedule C. since this is for additional work for services performed it's subject to self-employment taxes. if you get a 1099-Misc for your regular work, read no farther.
if you're an employee, you get a W-2, the stipend should have gone on it since it would be considered additional compensation. if this is the case you are really supposed to file IRS form 8919. It's a red flag to receive both a W-2 and 1099-Misc from the same employer. I should also inform you that filing the 8919 will likely result in the IRS contacting your high school as to why it wasn't on your W-2.
