Hayward firefighters say the man drove around the crossing arm after it dropped when the train was approaching.
It happened at West Tennyson Road and Leidig Court. The fire department couldn't find the car that was hit, but later located it on Pacific Street.
"He almost made it, but he got clipped by the train. The vehicle sustained rear-end damage but the man drove away without stopping," said Hayward police Sgt. Jason Corsolini.
Witnesses reported the collision and the vehicle's license plate was found at the scene, leading police to the man's home.
After interviewing the driver, officers determined that he seemed confused and couldn't answer questions clearly. They issued a citation and revoked his license on the spot due to safety concerns, Corsolini said.
No injuries were reported to the driver or to anyone on the train.
The train, which was traveling from Sacramento to San Jose, was held at the scene until 9:24 a.m. while inspectors checked the track, according to Amtrak spokeswoman Vernae Graham.
The man is ok. Train service was delayed by an hour and a half. The driver has been cited and his license suspended.
Bay City News contributed to this story.