Damage caused by the blaze at Cromwell High School in, Dukinfield, Greater Manchester, was "much more extensive" than first thought, staff said.
Classes at the school, which caters for pupils with special needs, are being held at another venue while repairs are carried out.
About 50 firefighters tackled the blaze on Yew Tree Lane on Friday.
A statement on the school's website said the whole school building would be "out of operation for the rest of the summer term" after surveys revealed the extent of the damage.
"This will mean that school will have to operate from another site and all the equipment that the pupils require will need to be moved," it said.
Three boys, two aged 14 and one aged 15, have been charged with arson with intent to endanger life.
They will appear at Tameside Youth Court later.
A fire-hit high school is going to be closed for the summer term, parents have been told.