The incident came to light after the father of the girl, living near Sola bridge area here, approached police when his minor daughter went missing at 10 AM yesterday.
While searching for the girl, police learnt that the victim was last seen with the young boy working as a cleaner with a private bus operator Jain Travels.
According to the complaint, the boy came to his house yesterday and asked for some water following which the girl went missing.
However, the boy denied of having raped the girl.
"We found the girl hidden in the luggage compartment. Her body was tied up with ropes and bore several cut marks near her neck and chest. It seems that the boy has raped her and then killed her to hide his crime," said Sola police inspector S M Patel. The body of the girl has sent for postmortem to ascertain whether she was raped, he said.