Police Officer Naveed Benjamin says the Tacoma-area family stopped at a gas station at about 12:30 a.m. Wednesday.
The father put his pistol under the seat and got out to pump gas while the mother went inside the convenience store.
They left the boy and a 4- or 5-year-old daughter in the car. The boy climbed out of his child seat, found the gun and shot himself in the head.
He was declared dead at a hospital. The girl was not injured.
It was western Washington's third recent shooting by a child.
Detectives questioned the parents and say the shooting is a tragic accident.