The manager of Alsalamskolan School said security footage shows the two masked men causing the fire to break out, Mugtama.com website reported.
They broke windows on the lower floor of the school and throw flammable materials inside on Sunday, he added.
The footage has been handed to the police who have launched an investigation.
No one was hurt in the incident as the arson took place in the early hours of morning when there were no students inside.