The victim's mother said the girl reported the incident the next day at her school, Martin De Porres Academy, but school officials did not report it to authorities, the New York Daily News reported.
The lawsuit alleges the girl, known by the initials K.J. was sexually assaulted for 10 minutes by two teenage boys, as an additional boy "hit her on the head whenever she tried to escape."
The Daily News said K.J. was the only girl in her class, and her alleged attackers all lived at a residence for juvenile delinquents.
Martin De Porres Executive Director Ed Dana said the school conducted an internal investigation and fired a teacher as a result.
"We want the community to know that we hold our teachers to a high standard. Our top priority is the safety and well-being of the children in our care," Dana said in a statement.