Officers arrested the teenager from Bell Post Hill at the scene.
Principal Scott Diamond cancelled classes at the campus today, telling the school community no on-site supervision would be available.
The fire caused significant damage to the main building, including campus administration and Prep to Year 2 classrooms, according to Diamond.
“Sadly, initial investigation points to arson. On the advice of emergency services, the Department of Education has confirmed that our Hendy Street Campus will remain closed on Tuesday,” the principal said in a statement.
“We will provide more information when it becomes available, particularly regarding arrangements for the rest of the week.”
The 13-year-old is currently in custody and is speaking to police.
Police have established a crime scene and investigations will continue.