The accident occurred about 4:19 pm along the Union Pacific tracks in Santa Clara.
Police Capt. Wahid Kazem said it isn't clear as to why the child was on the tracks or how the child got there, but stressed it was an accident and not a deliberate act. He couldn't provide the child's age.
Passenger trains operated by Amtrak and by the Altamont Corridor Express have been delayed as a result of the accident.
Amtrak's Capitol Corridor trains in and out of San Jose, as well as one eastbound ACE train destined for Stockton, have been held as the investigation continues.