The boy, a class VI student, has been arrested and a case registered under IPC section 302 (murder) against him, they said.
Six-year old Sivaram was found lying in the toilet of the school with bleeding injuries on his head this morning. He was rushed to a private hospital by the school authorities but declared brought dead, police said.
Investigations showed that the senior student had allegedly attacked the victim with the stone over some arguments the two had recently.
Authorities declared a holiday for the school while police personnel were deployed in the area as a precautionary measure as tension prevailed for some time after the incident.