Navarro was born in Santa Monica, California on June 7, 1967, the son of James Raul Navarro and Constance Colleen Hopkins. His paternal grandparents were Mexican immigrants. His grandfather Gabriel Navarro was close friends with Mexican silent film actor Ramón Novarro, who allegedly adopted his artistic surname. He attended Notre Dame High School in Sherman Oaks, California, where he was a member of the marching band with future Jane's Addiction bandmate Stephen Perkins.
Navarro's mother was murdered by her ex-boyfriend, John Riccardi, in March 1983. Riccardi was arrested in 1991, thanks to a viewer tip after Riccardi was featured on the television series America's Most Wanted. During his appearance on America's Most Wanted in 2004, Navarro stated that he was supposed to visit and stay with his mother on the night of her murder but at the last minute went to stay with his father. In 2015, Navarro released the documentary Mourning Son, which details his mother's murder and his spiral into drug addiction, as well as the pain he has had to overcome in the years since her death.
Navarro has been married three times: celebrity makeup artist Tania Goddard-Saylor (June 1990 – 1992, divorced), Rhian Gittins (October 15, 1994 – October 20, 1994, annulled), and model and actress, Carmen Electra (November 22, 2003 – February 20, 2007, divorced).
Navarro has stated he is supporting Marianne Williamson as a candidate for the 2020 Democratic presidential primaries.