Uma Shankar (22), Shaukin (24) and Sarafat (21), part of a six-person group had allegedly looted cash and valuables from passengers at knife point, police said, adding that five stolen mobile phones were recovered from them.
The incident occurred on January 16 while the train was waiting at the Yamuna Loha Bridge near Old Delhi Railway Station for green signal.
The three were arrested on Friday after Delhi Police's anti-snatching cell on a tip-off laid a trap at Kodiya Pul near Old Delhi Railway Station where the vagabonds were expected to meet, police said.
They claimed the suspects also disclosed their modus operandi, which was to target train coaches with less number of passengers. The accused used to board the coach from one station, loot the passengers at knife point and deboard the train as it slowed down at the outer signal before entering another station.
"Efforts are on to link other such crimes committed by them," the police said, adding that the suspects are vagabonds and stay near railway stations.
The nabbing of the three vagabonds follows the arrest of vagabonds for allegedly gangraping a Danish woman in the national capital.
Ever since the gangrape of a Danish woman near Old Delhi Railway Station, the Crime Branch has started keeping a watch over the activities of vagabonds staying near railway stations, police said.