The collision was reported at 7:31 a.m. near the intersection of Winslow and Vallejo streets, a Contra Costa County fire dispatcher said.
The person was transported by helicopter to John Muir Medical Center in Walnut Creek, the dispatcher said. He did not know the extent of the person's injuries.
There were 56 passengers on board the train at the time, which was heading from Sacramento to Oakland, Amtrak spokeswoman Vernae Graham said. No one on board the trains were injured.
Amtrak trains were delayed between Martinez and Richmond, Graham said. Tracks re-opened at about 8:45 a.m.