It happened just after 14:30 BST at a level crossing near Stretham.
A man, in his 40s, was treated by the East Anglian Air Ambulance and flown to Addenbrooke's Hospital in Cambridge.
The collision involved a Great Northern King's Lynn to London King's Cross train. The 4x4 was hit at the Nairn level crossing, off the A1123.
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British Transport Police said the male driver of the vehicle suffered serious injuries but they were not thought to be life-threatening.
Network Rail said the crossing was typically used by few than 10 vehicles per day and there were "clear instructions" telling people to phone a signaller to ask permission to cross.
Spokesman Ross Easton confirmed the signaller had not received a call prior to the incident and the telephone system had been working.
"Our thoughts are with the driver of the vehicle and his family and we will continue to assist with the ongoing investigation," he added.
About 115 passengers had to be transferred to another train after it was damaged in the crash.
A train struck a Land Rover on the railway line between Ely and Cambridge, prompting an investigation.