The incident occurred on Wednesday morning when the boy was relieving himself in an under-construction structure on the premises of the school, a police official said.
The boy was class 4 student. According to police, the boy was attacked with an axe on his neck and hips.
The victim's body was sent to the government hospital for postmortem.
Additional SP, Thane, Prashant Kadam said the motive behind the killing is not known immediately.
No arrests have been made so far, he said.