Police said the car crashed through a fence and on to the line as the 14.25 Plymouth to Edinburgh express was slowing on its approach to York station last night.
None of the Virgin service's 75 passengers or its driver was injured in the collision, which happened on the East Coast Main Line in the village of Copmanthorpe just before 9pm.
Today, the train was being pored over by engineers as it stood, still on the rails, beside a modern housing estate in the village.
There was visible damage to the underside of the lead locomotive but the rear loco and the three carriages appeared untouched by the accident.
About half a mile away, at the bottom of the narrow Moor Lane, further investigations were under way on the wreckage of the car, with officers from British Transport Police refusing to allow the Press and public close the scene.
People living close to where the train came to rest said they just heard a sharp bang.
On Moor Lane, those living in the nearest houses said the first they knew about the crash was the sounds of the emergency services arriving.
One woman said she was puzzled over how the car ended up on the tracks but said there used to be a level crossing at the bottom of the lane many years ago.
She said: "It seems he just went straight through the fence and on to the track.
"I don't understand it at all."
A spokesman for British Transport Police said the man who died was local.
He said: "A Virgin train travelling from Plymouth to Edinburgh collided with a car which had left a country road, crashed through a fence and on to the tracks.
"A 55 year old local male, believed to be the driver of the car, was found dead at the scene.
"The front carriage of the train derailed on impact with the vehicle. Luckily, there were no injuries to the passengers or staff on board.
"All 75 passengers were taken off the train and taken to a reception centre nearby at York station.
"The body has been removed from the scene and the British Transport Police are currently working to clear the line and remove the vehicle, which is trapped under the train.
"Two of the four lines have been reopened following the accident. Trains are able to travel along the section of the line in question. However, delays are expected. Passengers are advised to contact National Rail prior to travelling."
This morning, services were resuming on adjacent lines, with engines all sounding their horns at they passed the stricken service.
Virgin spokesman Arthur Leathley said the train had remained upright in the collision.
"The front wheels have come off the rails," he said.
"Technically, we call that a derailment, and that gives the impression of the train being on its side.
"But the amazing thing is that the train, travelling at 100mph, has stayed upright.
"These trains can do 125mph, but it was slowing down as it came into York.
"These are some of the newest trains on the network, and they underwent a lot of crash testing before they came into service.
"There is a crumple zone in the nose of the train that is designed to absorb a lot of the force of any impact and it appears that this is exactly what happened."
The collision has halted trains running between York and Leeds.
He confirmed the train driver was uninjured in the collision, and that the crash did not happen on a level crossing.
The incident at Moor Lane occurred at 8.55pm. North Yorkshire Police, British Transport Police, the fire service and ambulance crews all attended the scene.
The car had left the road, gone through a fence and ended up on the track, a police spokesman said.
Passengers taken off the train last night said the driver told them the train was doing 104mph at the time of the impact.
Dave Lamport, from Stockton-on-Tees, told the York Press: "It could easily have been another Selby but the driver was first-class."
Joe Horsfall, of Edinburgh, told the paper: "At first people were screaming but then they went quiet. No one was doing anything or panicking and we were just staring at each other."
The crash had echoes of the Selby rail crash in 2001 which happened little more than 20 miles away.
In that incident, a Land Rover driven by builder Gary Hart left the M62 motorway, plunged down an embankment and stopped on the East Coast Main Line at Great Heck near Selby, where it derailed a Newcastle-to-London high-speed service.
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