British Transport Police said the 67-year-old woman went through a level crossing barrier at Datchet, Berkshire, at 06:05 BST.
Her Volkswagen Golf collided with a train travelling from Clapham to Windsor and Eton Riverside station, where it was due to come into service.
A police spokesman said the woman was arrested on suspicion of dangerous driving and is in custody.
The train's driver and guard were not hurt. Passengers are facing delays because of the incident.
South West Trains' services are unable to run between Windsor and Eton Riverside and London Waterloo.
Buses have replaced trains and the disruption is expected to last until at least 12:00 BST.
British Transport Police said the incident would be the subject of a Rail Accident Investigation Branch inquiry.