The offer letter says $38,000. The fees office says something else. That gap is the whole subject of this article.
At most reputable US PhD programs, tuition is waived on top of the stipend. You do not pay tuition; the department covers it. This is standard, and any program that does not waive tuition for funded PhD students owes you a very good explanation. Ask for it in writing.
Fees are where it gets sneaky. Student fees, health fees, technology fees, a gym fee for a gym you will never set foot in. Some programs waive these too. Others leave you paying a few thousand a year out of your stipend, quietly. A couple thousand dollars is a meaningful pay cut on a grad student budget, and it never appears in the headline number. I have seen students blindsided by this in September, which is a terrible month to discover a pay cut.
Put the whole picture into a grad school budget planner app. Stipend in, then subtract every fee, every insurance premium, every cost the brochure skipped. Run a PhD funding comparison across your offers the same way. The program with the slightly smaller stipend and zero fees often wins, and it wins by more than people expect.
Health insurance deserves its own line in the spreadsheet. Some programs include a full plan. Some offer a plan you pay into. Some leave you on the marketplace. The difference can be thousands per year, and this is health we are talking about, not a perk. Treat it like salary, because that is what it is.
Then the quiet costs: international student fees, deposits, moving expenses nobody reimburses. Ask current students what they actually pay each year beyond the brochure. Students know. The brochure does not.
The rule is simple. Compare total compensation, not stipends: stipend plus tuition waiver plus fees covered plus insurance plus summer funding. The program pages at phdstipend.fyi lay out benefits alongside stipend figures, so you can see the whole package instead of the headline. Read the fine print before the fine print reads you.