The department says the blaze broke out around 3:15 p.m. on the third floor of the five-story Accion Academy at 1825 Prospect Ave.
It was under control as of 3:45 p.m. The fire was confined to a classroom, officials said.
The city Education Department did not immediately return a message.
According to the department's website, Accion Academy serves about 180 students in grades 6, 7 and 8.
The site said students usually go home around 2:30 p.m. but some stay on an extended schedule until 3:07 p.m.