"The train involved was a Trafford Park to Southampton freight service, and the driver is reported to be shaken but uninjured.
"Officers are working to establish the full circumstances, including how the car came to be on the tracks at the time."
Train passengers on Cross Country and First Great Western services were warned they face delays of up to an hour because of the crash north of Oxford, according to the National Rail Enquiries website.
Buses were replacing trains between Oxford and Banbury.
First Great Western said it was expecting disruption to continue into the early hours of Thursday morning.