The accident happened shortly after 9 p.m. Saturday night, at Figarden and Santa Fe. Fresno police say a female driver was crossing the area when the light turned red.
She panicked and stopped her car on the tracks.
The freight train conductor saw the car ahead and slowed down but still hit the car.
The woman is expected to be okay.
Officers say when they approached the car they could smell alcohol. Investigators are trying to find out if that was a factor in this accident.
This is the second time in two weeks that a train hit a car at the same intersection.