Two Sonoma County deputies on patrol saw the boy walking with what appeared to be a high-powered weapon on Tuesday in Santa Rosa in northern California, said sheriff's Lieutenant Dennis O'Leary.
They called for backup and repeatedly ordered him to drop the rifle, which resembled an AK-47 with a black magazine and brown butt, according to a photograph released by the sheriff's office.
Deputies only found out after the shooting that it was not a real firearm, Lt O'Leary said.
Rodrigo Lopez identified the boy as his son, Andy Lopez, to a newspaper and said the teenager had been carrying a toy gun that belonged to a friend.
It was not clear whether the boy pointed the replica assault rifle at the deputies or made any type of threatening gesture.
Lt O'Leary said the deputies fired several rounds from their handguns immediately after issuing the orders to drop the rifle.
A neighbour in the area, Brian Zastrow, told the Santa Rosa Press Democrat newspaper that he heard seven shots.
"First, I heard a single siren and within seconds I heard seven shots go off, sounded like a nail gun, is what I thought it was," he said.
Lt O'Leary said the boy fell to the ground on top of the rifle and deputies ordered him to move away before approaching him and putting him in handcuffs.
They then began administering first aid and called for paramedics, who pronounced the boy dead at the scene.
Deputies also found a plastic handgun in the boy's waistband, Lt O'Leary said.
The deputies, who have not been identified, have been placed on administrative leave, which is standard after a shooting.
Community members left candles, teddy bears and flowers at the edge of the field where the teen was shot and questioned deputies' decision to open fire.
"I'm sure you can tell he's a 13-year-old boy," Abrey Martin told KGO-TV. "He's not some maniac."
The Press Democrat quoted the boy's mother, Sujey Annel Cruz Cazarez, as saying, "Why did they kill him? Why?"
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