Police say 35-year-old Daniel Reilly carried on a more than nine month affair with a former student that began when the girl was 14 years old.
Reilly was arrested at IS 237 in Flushing, Queens, where he works as a sixth-grade English teacher.
Police say the suspect taught the girl when she was in elementary school, and she is not presently a student at the school where he now teaches.
The child's parents called police Monday after the girl's sister read a series of sexually-explicit text messages between Reilly and the victim.
The sexual encounters allegedly took place at Reilly's Forest Hills residence between August 2012 and April 2013.
"This case is particularly disturbing," Queens District Attorney Richard Brown said. "Schools should be safe havens for children. Instead, this defendant is accused of sexually preying upon one of his former students and rendezvousing with her at his residence."
Reilly is charged with four counts of second-degree rape, two counts of second-degree criminal sexual act, one count of endangering the welfare of a child and six counts of third-degree sexual abuse.
Bail was set at $30,000. If convicted, he faces up to seven years in prison. Reilly is due back in court on May 6.