Police said the two children were alone together in the officer's parked van when they found a gun in the glove compartment. They took out the weapon and were handling it when the boy accidentally shot the girl.
Police and medics responded to the scene, in the 10200 block of 270th Street NW, near Stanwood City Hall, at about 3:30 p.m. after receiving reports of the shooting.
The injured girl was rushed to Providence Hospital in Everett as medics administered CPR. Her condition was not available Saturday night.
The children's parents reportedly were nearby but not inside the van at the time of the shooting.
It was not known whether the gun was the officer's duty weapon or a personal firearm. The age of the boy who pulled the trigger was not released.
"At this time we are all extremely concerned for the well-being of one of our department family members," Marysville Police Chief Rick Smith said in a written statement. "Our thoughts and prayers are with him and his family, especially his injured little girl."
Witnesses at the scene said there was a heavy police response to the incident, and the area was sealed off with crime tape while police collected evidence.
Detectives from the Snohomish County Sheriff's Office Major Crimes Unit are handling the investigation.