The accused (13) has been detained, they said.
The incident happened last evening when the boy, working at a roadside eatery in Amerbath township of Thane, lured the girl on some pretext and took her to an isolated place where he allegedly raped her, Ambernath police station sub-inspector Manisha Mane said.
Both the accused and victim live at the Datta Nagar slum colony of Chikloli locality in Ambernath.
The girl returned home crying and told her mother about the assault after which she lodged a complaint with police.
An offence under section 376 (rape) of the IPC has been registered against the accused, police said, adding he has been sent for a medical examination to JJ hospital in Mumbai.
The victim has also been sent for medical examination, police said, adding further investigation is on.