Police say 44-year-old Charles Oross, a teacher at IS 238 in Queens, engaged in sexual contact with the girl while she attended the school.
He and the victim also allegedly had inappropriate email and Facebook exchanges.
District Attorney Richard Brown said that, according to the criminal charges, Oross engaged in sexual activity with a female student in a classroom and in his vehicle, on multiple occasions between January 2009 and April 2010, beginning when the student was 13 years old.
Oross, of East Islip, is charged with rape, criminal sexual act and endangering the welfare of a child.
If convicted, he faces up to four years in prison.
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