The incident took place on November 27, said inspector Balkrishna Wagh of Ambarnath police station.
The accused Sinu Sriram Avadh Rathod entered the girl's house at around 8.30 in the evening when she was alone and raped her.
The girl, who can not speak, could not raise alarm, but conveyed the incident to her parents later when they returned home.
The accused hails from Uttar Pradesh, police said.
As the girl is a minor, police have also pressed charges under Protection of Children From Sexual Offences Act, 2012, apart from the charge of rape under the IPC.