The body was discovered in Swaroop Nagar area at around 3 AM and the deceased has been identified as Rohan, an LKG student, police said.
A villager informed the police after he found the semi-buried body inside a pit.
Rohan was missing since March seven and a case kidnapping was registered.
A senior police official said they suspect that the boy was murdered because his skull had fractures.
"It appears to be a case of personal enmity. The family had not received any ransom call," the official said.
The incident comes days after two siblings, Mansij (7) and his sister Yashbi (5), who were kidnapped from their school, were found dead in a jungle. The kids' uncle and his two frineds have been arrested on murder charges.