The deceased, identified as Akash Behera, a Class IV student of Narayanpur, a nearby village, was missing since Wednesday afternoon. He was not seen after he played with others in the village.
Family members and villagers searched him as the boy did not return to the house in the evening. The boy's body was found from the abandoned toilet in the school, said sub-divisional police officer (SDPO) Aska Sarah Sharma.
"We are pressing the scientific team and dog squad for investigation of the murder", Sharma said
Balaram Behera, the father of the deceased boy, works in Surat in Gujarat. His mother Namita lodged a complaint at the local police station.