The Sonoma County deputy shot Andy Lopez Cruz Tuesday when he mistook a replica AK-47 for a real one.
The FBI informed Sonoma County Sheriff Steve Freitas and Santa Rosa Police Chief Tom Schwedhelm Friday it will conduct an inquiry separate from the one local police are conducting, The (Santa Rosa) Press Democrat reported.
"It's a civil rights-type of case," said FBI spokesman Peter Lee in San Francisco.
Schwedhelm said police will cooperate with the what the newspaper said will be the first FBI investigation of an officer-involved shooting in the area since 1997.
The deputy said he believed the boy was holding a real rifle and that he called on Cruz twice to put it down. He said the teenager was turning toward him when he opened fire.
Cruz, who was shot seven times, was carrying a replica AK-47 that fires plastic pellets instead of bullets.
About 300 people, many of them teenagers, marched in Santa Rosa Friday to protest Cruz's killing.
Some of them had been allowed to skip high school classes to participate, the San Francisco Chronicle reported. The march route went past the school, where protesters called on students to join them, and ended at the Sonoma County Sheriff's Office.
Seana Ramirez told the Chronicle her son, who has never previously been interested in political protest, asked her permission to march.
"The kids are pissed off, and they want their voice heard," Ramirez said. "If the kids are the future, they should have the loudest voice and we should listen."
Robert Edmonds, a law enforcement watchdog, told The Press Democrat a civilian review of the killing should be conducted.
Law enforcement officials say a civilian grand jury already fills that role.
The Sonoma County chapter of the American Civil Liberties Union says an independent investigation is needed to "supply the facts needed for corrective recommendations and give the public confidence in the actions of the agents pledged to protect our community."