The alleged incident took place on the Northeast Express last night.
The 28-year-old woman had boarded an AC coach of the train at Allahabad for Delhi, GRP Inspector Tripurari Pandey said.
The woman has alleged that as the train started from Allahabad, the three jawans, who were already in the coach, came and sat on the seat in front of her.
They then started misbehaving with her, Pandey said, adding that the accused were drunk at the time of the incident.
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Near the bathroom, the woman saw a sticker on a train door containing the women helpline number of the Kanpur GRP.
She called up the helpline and the GRP personnel arrested the accused as soon as the train arrived here.
The accused have been identified as Rishipal Singh, Arun Kumar and Manoj Kumar.
"They were taken into custody and sent for medical examination which proved that they were drunk," Pandey said.
"All of them have been arrested and the Army has been informed about the incident. Further action will be taken after Army officials arrive here," he said.