Metra said inbound train #2124 struck a vehicle in the Ingleside area near the intersection of Wilson Road and Larkin Lane.
Metra announced a series of changes to its service due to the crash.
At last check, trains were operating with a 15-to-25-minute delay at Grayslake and Fox Lake.
The sheriff's office and Fox Lake police are at the scene of the crash.
It was not immediately known how many people were on the train at the time of the crash.
The crash happened before 8 a.m., according to Metra.
Metra police is handling the investigation.
This is a developing story.