Both men were pronounced dead at the scene.
"This is not a spot where we frequently see people," said Sainte-Thérèse police spokesman Jonathan Germain.
At that location, the train runs below Highway 640. The accident occurred in the south end of the tunnel, according to Germain.
Canadian Pacific Railway officials were on the site to check the Blainville-St-Jérôme tracks.
The Agence Métropolitaine des Transports (AMT) set up a shuttle bus service for commuters until the track cleared nearly four hours later.