Nicholas Thomas Jones, 32, appeared in court to enter the plea and was ordered held on $3 million bail.
Los Angeles County Sheriff's deputies arrested Jones after they say his son Princeton Jones was shot to death in the backyard of his grandfather's house in West Rancho Dominguez over the weekend.
Family members described Princeton as funny, caring and said he adored his mother. A GoFundMe account has been set up to help his family.
A vigil was held Sunday to honor the boy.
9-year-old boy shot and killed while at grandfather's house in Compton, family says
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.
The sheriff's department initially identified the location of the shooting as Compton, but later said it was West Rancho Dominguez, an unincorporated community just to the west of Compton.
A preliminary hearing has been set for Jan. 7.