Skokie police said a car disregarded lowered crossing gates just before 1 p.m. at the crossing at Niles Center Road and was hit.
Police said no one was injured, but the train operator was taken to a local hospital for evaluation.
Video of the scene showed an SUV with rear-end damage.
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Passengers were seen being evacuated from the train involved.
Shuttle buses were requested from Skokie to Howard to provide connecting service through the area while Yellow Line trains were stopped, the CTA said.
Service resume just before 4 p.m.