The incident occurred in a toilet of a sleeper coach of Amarkantak Express (Durg-Bhopal) yesterday.
"The woman is an unauthorised vendor who sells popcorn on train," Habibganj Government Railway Police (GRP) incharge sub-inspector BL Sen told PTI.
The woman hails from Budhni in Sehore district of the state.
He said the accused has been identified as Jitu (25) who hails from Bhopal.
No arrest has been made in the case so far.
After the woman confided in her husband, the latter lodged a primary complaint with the Budhni police station which was eventually shifted to Habibganj, the officer said.
"We have registered an FIR and booked the accused today under sections 376 (rape) and 506 (punishment for criminal intimidation) of the IPC and have launched a hunt to arrest him," the SI added.