The girl, from Kaman village in Vasai area of Thane district, had left for her school on January 16, but did not return home.
Later, her family members, after carrying out a search in vain, lodged a missing complaint with the local police, Waliv Police Station inspector Rajendra Mohite said.
Police received information about a body lying at a farm in the village. The police rushed to the site and later the decomposed body was identified as that of the missing girl.
Police said the body was sent for postmortem which revealed that the girl had been raped before being killed.
Offences have been registered against unidentified persons under sections 302 (murder) and 376 (rape) of the IPC along with relevant sections of the Protection of Children from Sexual Offences Act, 2012, police said, adding that search for the culprits was on.