U.S. District Judge Cormac Carney cited the small number of people who have actually been put to death since the state adopted its current law in 1977 and the long delays between sentencing and execution.
The judge described the 13 people executed as a "random few" and said "random factors" make the difference between life and death. He said neither retribution nor deterrence are served because of the years between crime and punishment.
"No rational person can question that the execution of an individual carries with it the solemn obligation of the government to ensure that the punishment is not arbitrarily imposed and that it furthers the interests of society," Carney said.
Carney ruled in a case brought by Ernest Dewayne Jones, who has been on death row for almost two decades. Jones, a convicted rapist, was sentenced in Los Angeles in 1995 for raping and killing his girlfriend's mother, Julia Miller, three years earlier and 10 months after he had been paroled.
Since 1977, about 900 people have been sentenced to death in California. More people have died on death row from natural causes and suicide than from execution.
Natasha Minsker of the American Civil Liberties Union of Northern California said Carney's ruling is "the first time any judge has ruled systemic delay creates an arbitrary system that serves no legitimate purpose and is therefore unconstitutional."