Senior police inspector G B Thorat, of the Thane railway police station told PTI that the victim Tushar Jadhav (22) was among students who were studying in an engineering college at Ratnagiri.
The group of students were returning home from college by the Konkan Kanya Express.
According to the police, got down at Panvel and took the first train bound for Thane to go to Airoli and boarded the luggage coach just next to the ladies compartment.
When the train reached Thane railway station, they saw that his throat had been slit. The victim was rushed to the Thane Civil hospital where doctors declared him brought dead.
The Thane railway police has registered an offence under Section 302 of the Indian Penal Code and transferred the case to the Navi Mumbai railway police at Vashi, the police said.
The police said that it is inspecting CCTV footage at Ghansoli station to identify the killers.