Iqra Public School at Dooru Anantnag was set on fire by unknown persons, a police official said, adding the upper storey of the building was destroyed.
He said police and Fire and Emergency Services personnel rushed to the spot and doused the flames.
The total number of educational institutions destroyed in arson since the unrest began in Kashmir in the aftermath of Hizbul Mujahideen militant commander Burhan Wani on July 8, has gone up to 20.