Stayner was born and raised in Merced, California. His younger brother, Steven, was kidnapped by child molester Kenneth Parnell in 1972, when Cary was 11, and held captive for more than seven years before escaping and being reunited with his family. Cary Stayner would later say that he felt neglected while his parents grieved over the loss of Steven.

When the decapitated body of the fourth victim Joie Ruth Armstrong was found, eyewitnesses said they saw a blue 1979 International Scout parked outside the cabin where Armstrong was staying. Detectives traced this vehicle to Stayner. This caused Stayner to become the prime suspect in the case. FBI agents John Boles and Jeff Rinek found Stayner staying at Laguna del Sol nudist resort in Wilton, where he was arrested. His vehicle yielded evidence linking him to Joie Armstrong. During his interrogation, Stayner confessed to the four murders as well as to sending the map for finding Juli Sund's body.

When Steven escaped from Parnell and returned home in 1980, he received massive media attention; a true crime book and TV movie, both titled I Know My First Name is Steven, were made about the ordeal. Steven died in a motorcycle accident in 1989. The following year, Stayner's uncle Jesse, with whom he was living at the time, was murdered. Stayner would also later claim that his uncle molested him when he was 11.

Stayner is reported to have attempted suicide in 1991, and was arrested in 1997 for possession of marijuana and methamphetamine, although these charges were eventually dropped.

In 1997, Stayner was hired as a handyman at the Cedar Lodge motel in El Portal, just outside the Highway 140 Arch Rock entrance to Yosemite National Park. Between February and July 1999, he murdered two women and two teenagers: Carole Sund; her daughter, 15-year-old Juli Sund; their travel companion, 16-year-old Argentine exchange student Silvina Pelosso; and Yosemite Institute employee Joie Ruth Armstrong, 26, a naturalist. The first two victims, Carole Sund and Silvina Pelosso, were found in the trunk of the charred remains of Carole's Pontiac rental car. The bodies were burned beyond recognition and were identified using dental records. A note was sent to police with a hand-drawn map indicating the location of the third victim, Juli Sund. The top of the note read, "We had fun with this one." Investigators went to the location depicted on the map and found the remains of Juli, whose throat had been cut.

He was convicted of the murders of four women between February and July 1999: Carole Sund, her teenage daughter Juli Sund and their teenage traveling companion Silvina Pelosso, and Yosemite Institute naturalist Joie Ruth Armstrong. The murders occurred in Mariposa County, California, near Yosemite National Park. Cary Stayner was sentenced to death for the four murders, and remains, as of March 2018, awaiting execution on death row at San Quentin Penitentiary in California.

Stayner pleaded not guilty by reason of insanity. His lawyers claimed that the Stayner family had a history of sexual abuse and mental illness, manifesting itself not only in the murders, but also his obsessive-compulsive disorder, and requested to be provided with child pornography in return for his confession. Dr. Jose Arturo Silva testified that Stayner had mild autism, obsessive-compulsive disorder, and paraphilia. Stayner was nevertheless found sane and convicted of four counts of first degree murder by a jury in 2001.

In 2002, during the penalty phase of his trial, he was sentenced to death and thereafter entered housing in the Adjustment Center on death row at San Quentin Penitentiary in California. Stayner remains on death row as of June 2016, though San Quentin's gas chamber has been dormant since a 2006 judicial action called California executions to a halt over perceived flaws in process (and a more recent ruling by federal Judge Cormac Carney ruled that state’s death penalty unconstitutional because of legal issues raised by the penalty's disuse).