The incident happened just after 7:30 p.m. Saturday on Haskins Avenue, near Visalia Avenue, according to the Los Angeles County Sheriff's Department.
Deputies found the boy, identified by his mother as Princeton Nicholas Jones, suffering from a gunshot wound in the backyard of the home. He was pronounced dead at the scene.
Detectives honed in on the boy's biological father as the suspect. Nicholas Jones, 32, was arrested Sunday for murder and child abuse resulting in death.
The boy's mother, Creole Green, said her son had autism.
"My goal... was to give him the proper teachings and all the things that he needed in order to navigate this world independently one day," Green said. "I'm just devastated that my son's life... the door was shut in front of him at nine years old."
9-year-old boy shot and killed while at grandfather's house in Compton, family says
The boy's mother added that he was staying at his grandfather's house when the shooting happened.
Family members described Princeton as funny, caring and said he adored his mother.
A GoFundMe account has been set up.
A vigil was held Sunday to honor the boy. Community leaders called for an end to the violence.
"This is our community," said Paulette Gibson, president of the Compton NAACP. "It is unfortunate that our young people can't feel safe in their own community."
Additional details about the deadly shooting were not available.