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Short Answer: If you are still student employed by the school, you don’t; otherwise you do.
All the F-1 visa holders need to pay taxes as resident aliens after fifth year. According to the IRS file Social Security/Medicare and Self-Employment Tax Liability of Foreign Students, Scholars, Teachers, Researchers, and Trainees, all the resident aliens need to pay FICA Tax (medicare and social security):
“Foreign students in F-1, J-1, M-1, Q-1 or Q-2 nonimmigrant status who have been in the United States more than 5 calendar years are RESIDENT ALIENS and are liable for social security/Medicare taxes (unless they are exempt from FICA under the “student FICA exemption” discussed below).”
However, there’s an exception for the resident alien F-1 visa holders who are still students employed by the school, according to the IRS file Student Exception to FICA Tax:
“FICA (Social Security and Medicare) taxes do not apply to service performed by students employed by a school, college or university where the student is pursuing a course of study. Whether the organization is a school, college or university depends on the organization’s primary function. In addition, whether employees are students for this purpose requires examining the individual’s employment relationship with the employer to determine if employment or education is predominant in the relationship.”
Update: Through the communication with the tax specialist of the school, they confirmed that the resident alien students should not be taxed on medicare and social security during the semester. However, if the resident alien students earn research assistantship during the summer, they will be taxed since the summer research “is not pursuing a course”.