The 17-year-old victim was reportedly a student at the school and is expected to survive.
The shooting left students at the school shaken, as those that returned to school on Thursday waited in lines for officers to screen them with metal detectors.
The alleged shooter is facing attempted murder, assault, and weapons charges. A security video from the scene appeared to show the shooter ride up on an electric scooter and open fire.
The school was briefly placed under a safety lockdown by police before it was lifted at around 3:15 p.m. and students and staff were allowed to leave.
It is currently unknown what led to the shooting but on Thursday the NYPD said that the victim appeared to not be the gunman's target.
Police say that two teens who were taken in for questioning shortly after the shooting were released and were not involved in the shooting.
Police have seized more than 4,700 weapons in city schools since the return of in-person classes in the fall.