The five-year-old girl, a distant relative of the accused - Krishna Isame - was playing outside her house in Wadachapada hamlet of Thane yesterday afternoon, police said.
Isame, who lives in the neighbourhood, called the girl inside his house and raped her, Assistant Police Inspector M B Supe said.
The girl informed her parents about the offence last evening following which they lodged a complaint against the accused, the official said.
Later, the accused was arrested and charged under section 376 (rape) of the IPC and sections 5 and 6 of the Protection of Children from Sexual Offences Act, he added.