Two others, including a child, were also injured in the incident
Contra Costa County fire protection district said three people were declared dead at the site of the accident.
The three killed have been identified as three women, all in their 50s.
A child and two men were also hospitalised with serious injuries.
The two injured men and the child were taken to John Muir Medical Center, local media reports said.
There were around 80 passengers onboard the train, but no one was injured in the incident.
Authorities said the incident took place at around 1pm local time in the 3000 block of Orwood Road on a dirt road in Brentwood, about an hour’s drive from San Fracisco.
The four-door sedan had pulled into a long rural dirt driveway when the Amtrak train struck it, reported The Mirror.
The car came to a rest about 60 feet away from the tracks.
“It’s not uncommon that we’ve had accidents at that crossing,” East Contra Costa County Fire Protection District public information officer Steve Aubert was quoted as saying.
Local reports said that two bodies were found lying on a gravel embankment 25 feet away.
Fatima Jimenez who was attending a fundraiser nearby said that she heard the sound of the crash and went to the site to find two women and a child lying in a pool of blood.
“People fainted when they heard what was going on,” she said to local media.