How do fee-waiver or teaching assistant programmes work for MS in Computer Science applicants at public universities in California?

You should separate two very different things here, the application fee waiver and the Teaching Assistantship funding you might get once enrolled. Most international MS in CS applicants will not qualify for a fee waiver, but a TA role after admission can meaningfully cut your ongoing tuition cost.

Fee Waivers Versus TA Funding

UC Versus CSU For MS Students

• At UC schools, PhD students get funding priority, so MS students often find TA roles easier to secure from semester two onward rather than immediately.
• At CSU schools, since most lack PhD programs, MS students are the primary TA candidates, though pay is often hourly rather than a full tuition waiver.
• International and out-of-state UC students must still budget separately for the Non-Resident Growth Tuition surcharge, since a standard TA appointment does not waive it.

My Advice

Do not count on an application fee waiver, but do budget realistically for your first semester before any TA income arrives, especially the non-resident tuition surcharge if you are targeting a UC school. Start applying for TA and research assistant roles the moment you accept your offer, and also check CSU campuses for Instructional Student Assistant postings, which are often easier to land early.