The accident happened at about 6.25pm yesterday when the Doncaster to Scarborough service struck a vehicle on the manually operated crossing close to the village of Rawcliffe Bridge near Goole.
The person who died was in the car and five of the people on board the train were taken to hospital with spinal injuries, a spokesman for British Transport Police said. Twelve other passengers were unhurt.
A witness, Maurice Champeau, told BBC News 24: "It is a manual level crossing, it's always been a bone of contention with the locals in the area, about whether the lighting on it has ever been adequate."
Mr Champeau said the victim was "local to the area", but could not confirm the man's identity.
Referring to the crossing, he said: "It is a talking point in the area, it has been a concern of theirs for some time." He said the train had not derailed and added: "It appears to be still on the tracks, but has travelled some distance from the actual accident."
The accident took place about eight miles from Great Heck, the scene of the Selby rail disaster in 2001, in which 10 people were killed after motorist Gary Hart fell asleep at the wheel of his Land Rover and plunged off the M62 on to the east coast mainline. A southbound GNER express train then collided with his car before being deflected into the path of a northbound coal train.