Fire officials say one of the trains was stopped and unloading passengers around 10 p.m. Wednesday night when the second train ran into it.
The train was going about 15 to 20 miles per hour.
Authorities say up to 18 people were hurt.
Officials say most of the injuries were minor, but several people were taken to local hospitals.
Amtrak says the collision was at low speeds between a "San Joaquin" line train that runs from Bakersfield to Oakland, and the "Coast Starlight", a train from Los Angeles to Seattle,
The "San Joaquin" train would have stopped in valley cities including Fresno, Madera and Merced.
The wheels of each lead engine reportedly went off the track.
Crews are still trying to determine what caused the collision.