The accused identified as Suraj (25) took the girl, who was playing outside her house, to a secluded place on Monday on the pretext of getting her snacks, and raped and killed her there, DCP K Rastradeep said.
When the girl did not return till late night, her parents informed the police and a search was initiated, he said, adding, Suraj was suspected as he was roaming around when the girl was playing with other kids.
According to police, the body was recovered from the crime scene, which is an abandoned structure.
"He killed her by slitting her throat open with a blade and covered the body with garbage," they said.
Suraj is an accused in a 2012 murder case and is currently out on bail.