Rafael Sosa, 29, who teaches at P.S. 208 on West 111th St., was arrested Wednesday and is accused of assaulting the girl several times, the Times reported.
The arrest is the latest in a string of alleged sexual abuses in city schools.
Last month, 35-year-old Brooklyn teacher Erin Sayar was accused of having a sexual relationship with a 16-year-old male student.
In March eight other teachers were accused of having inappropriate relations with students after a Department of Education review of personnel files dating back to 2000 to ferret out educators with a record of misconduct with students.
Sosa was expected to be arraigned in Manhattan on Thursday.
The Department of Education did not immediately respond to a request for comment.