Metra said the crash happened near Bryn Mawr in Gladstone Park.
A woman drove the van around the track barriers, and the train stuck her vehicle.
Video shows the heavily damaged vehicle sitting on the tracks.
The woman, who suffered non-life-threatening injuries, was taken to Lutheran General Hospital.
Metra service on the Union Pacific Northwest line was experiencing delays earlier Saturday, but service has since returned to normal.
Editorial note: This story initially said a woman died in the crash, based on information from a Metra spokesperson.