Women Police Sub-Inspector Ashwini Raut of Bhiwandi police station said the 13-year-old victim and the accused knew each other.
On November 5, one of the accused Vijay Yadav (19), an auto driver, took her to his room in Anjurphata area and raped her, Raut said.
He threatened her of dire consequences if she narrated her ordeal. On November 12, he again took her to his room and raped her, the officer added.
Later one of Vijay friend's Sandeep Patil (30) came to know about the incident when he had visited Vijay's house, she said.
A case under relevant sections of the Indian Penal Code and the Protection of Children from Sexual Offences (POCSO) Act 2012 was registered, she said, adding the duo was produced before a magistrate who remanded them to police custody till December 26.