The matter came to light last evening when the victim lodged a complaint against accused Shakeel Abdul Ansari and Santosh.
While Ansari was arrested, the other one is still at large. Police have launched a manhunt for him.
The victim worked in a factory in Boisar industrial estate and the accused had befriended her there. Later, she moved to Nalla Sopara following which on May 22 one of them called her to Boisar railway station for a meeting.
At the railway station the girl was fed a vadapav, which was possibly laced with sedatives. She fell unconscious and the duo took turns to rape her, the complaint said.
The police have charged both the youths under various sections of the IPC and sections 3, 4 and 8 of the protection of children from Sexual Offences Act, 2012.