A Queens high school gym teacher was arraigned Tuesday on charges that she raped a 16-year-old student last year.

Joy Morsi, 39, of Massapequa, L.I., allegedly had multiple sexual encounters with the male student, who was 16, between June and July 2013, according to the Queens district attorney.

She allegedly had sex with the student at several locations within Grover Cleveland High School.

Morsi was charged with 41 counts, including third-degree rape, third-degree criminal sexual act and endangering the welfare of a child, and was held on $25,000 bail. If convicted, she faces up to four years in prison.