The incident occurred on Tuesday when Shaikh Afroz Amin and another teenage boy were fighting on some issue on the campus of the school, said Shivlal Purbhe, inspector of Khuldabad police station.
The deceased was the resident of Rabale in Thane district adjoining Mumbai.
Police had initially registered the case as accidental death, but later booked the juvenile for murder after a CCTV grab purportedly showed him beating up Amin.
However, when he reached the hospital he was shocked to learn that his son had died.
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"The boy's father lodged a complaint with us saying that his son did not die a natural death," the inspector said.
During the course of investigation, police found the CCTV footage of the purported assault.
Further investigations are on, he added.