An Ottawa-bound train hit and killed a pedestrian around 12 p.m., about 20 minutes after leaving the Kingston station, Via Rail confirmed.
The train, which was carrying nearly 400 passengers, was scheduled to continue on to Montreal after Ottawa.
Trains were backed up in both directions between Toronto, Montreal and Ottawa on Sunday but were gradually back on the move as of 4:30 p.m. local time, said Via Rail spokeswoman Mylène Bélanger.
"All of our thoughts go to the victim's family," Bélanger said. "This is a tragedy."
The CN Police Service said the pedestrian was not struck at a rail crossing. Kingston Police have taken over the investigation.
The pedestrian was hit on a portion of the track that runs adjacent to the Cataraqui River south of Highway 401. It's a heavily wooded area with some marshland.