The victim was on her way to Siwan to meet her sister on March 5 during which she met a youth Pintu of the same village, Government Railway Police said.
She alleged that at Bhatni railway station Pintu took her to the toilet and raped her, it said.
The GRP said the victim alleged that later Pintu fled to Gorakhpur.
On the victim's complaint, a case was lodged yesterday and Pintu had been sent to jail.