The incident happened on the West Coast Express on January 11 and the youth has been identified as 22-year-old Chandan Kumar, a native of Bihar, police said.
Kumar, a carpenter by profession and working at a furniture store in suburban Kundrathur, was returning after an official visit to Mangalore.
Soon after the train reached Chennai, the victim lodged a complaint and the perpetrator of the alleged crime was arrested, police said, adding, he was remanded in judicial custody today.
Asked about the antecedents of the accused, investigating officer Saravanan told PTI that this seemed to be his first crime.
The victim was on a visit to the heritage town of Mahabalipuram near Chennai, he added.