The lawsuit, which claims Stephen was assaulted, seeks unspecified damages. The NYPD said the incident was "an unfortunate accident," not an assault. The officer was not disciplined.
Stephen said the officer was known for being aggressive with students.
"Students should be able to trust those assigned to protect them," he said Thursday at a news conference. "This incident has hurt me and made me question the ability of the educators and police personnel at my school to keep me safe."
The teen said he and Officer Daniel O'Connell had a verbal encounter in the hallway before the bathroom incident. Afterward, Stephen went to the nurse's office, and his parents were called.
Stephen said he felt uncomfortable around the officer after that. The two did not speak again, and the officer moved to a different school several weeks later.
The union representing city school safety officers, Teamsters Local 237, said the incident is "simply under investigation."
"We stand by our members," President Gregory Floyd said.
The city law department said it hadn't yet received the legal papers but would review them thoroughly.
Principals do not have the authority to discipline safety officers, said the family's lawyer, Jeffrey Rothman. They were put under NYPD control nearly a decade ago. The roughly 5,000 officers can make arrests but don't carry weapons.
The New York Civil Liberties Union also filed an internal complaint with the NYPD Thursday on Stephen's behalf.
NYCLU Executive Director Donna Lieberman said the incident highlights a need to give school officials more control. She called on the City Council to pass a law requiring police to give quarterly reports on the number of student arrests and school safety issues.
The law also would allow the Civilian Complaint Review Board to receive complaints against school safety officers. Currently, those complaints are logged with schools or local precincts.
More than 1 million students attend the city's public school system, making it the nation's largest.
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