Monsignor Scanlan High School in Throgs Neck will reopen after structural engineers inspected the building to make sure it was safe for students.
Officials say the damage was contained to the boiler room and two science labs.
The building will have heat and water, and damaged areas will be boarded up.
There is no school Monday because of the Martin Luther King, Jr., holiday.
Authorities are still investigating the cause.
Investigators say the blaze, first noticed by the principal, started in the boiler room about 6 p.m. and spread to the third floor. No students were in the building at the time, and the faculty got out safely.
Firefighters battled the flames as the fire tore through walls, floors and pipes, eventually reaching the altar of the third floor church.
"It was just a long tedious process," FDNY Assistant Chief William Seelig said. "They were chasing fire from one floor to another, but they were able to cut the fire off before it extended into the main five-story building."
The principal, Dr. Patrick McGuire, noticed fire in the school's two story boiler room and called 911.
"It was a fast-moving stubborn fire that spread in concealed spaces that were hard to access," Seelig said.
They eventually got control of the fire, but not without firefighters suffering some minor injuries.
Firefighters are calling the fire suspicious until they determine a definitive cause.