The blaze, in a third-floor classroom of PS 175 on West 134th Street, broke out just after 10:30 a.m. Monday, fire officials said.
It forced the evacuation of the entire school when smoke spread through the building. It was not clear how many students were in the school at the time.
School officials relocated students to PS 92 on West 118th Street and PS 96 on East 120th Street for the rest of the day.
The source said the girl - whose name was being withheld - wanted to avoid classes.
She was charged with arson, reckless endangerment and criminal mischief.