Police responded to reports that a pedestrian had been struck by the train in Geneva on Monday, the Chicago Tribune reported.
The victim was found on the tracks and pronounced dead at the scene. He has yet to be identified, say officials.
The grim accident closed a section of the Union Pacific-operated line for almost four hours.
Union Pacific spokesman Mark Davis said a 142-car coal train heading east from Wyoming to a utility in Wisconsin struck a “trespasser” west of the Geneva Metra station, the Sun Times reported.
The train had three locomotives and all cars were loaded with coal, Davis noted.
It was not clear who owned the freight train.
Also on Monday, Union Pacific launched a billboard campaign aimed at encouraging Chicago pedestrians to cross tracks only at approved railroad crossings.
The billboards show either a crossing arm with the message "Always Expect A Train", or a person about to cross tracks despite an oncoming train with the warning "Some Shortcuts Cut Your Life Short".
UPR said the 11 billboards were expected to be viewed by about 529,000 Chicago residents daily.
"These billboards will remind people of their surroundings and keep them safe around railroad tracks," said Wes Lujan, the region’s assistant vice-president of public affairs.
"Trains are operating at all times on railroad tracks, and our number one priority is the safety of our employees and communities."