Jose Lopez, 36, filed the lawsuit four years ago against the organization that runs the church, the Watchtower Bible and Tract Society of New York, saying he was molested in 1986.
According to Lopez, he was seven years old when he was molested by church leader Gonzalo Campos while a member of the Spanish congregation in the Linda Vista section of San Diego.
"It's never going to be over for me," Lopez told reporters during a press conference on Friday. "It was just a horrible thing and I want people to know what happened to me," he said.
Seven other people, six men and one woman, also claim they were molested by Campos and settled out of court.
Mario Moreno, a lawyer for the church, called the decision by San Diego Superior Judge Joan Lewis "drastic" in a statement and said the church would appeal.
"Jehovah's Witnesses abhor child abuse and strive to protect children from such acts," the statement said.
Lopez's lawyer, Irwin Zalkin, told reporters the Jehovah's Witness church has a culture of secrecy.
"These guys will deny and deny, they are belligerent, they are arrogant, they treat victims as adversaries," he said.
Zalkin said the church allowed Campos to work with Lopez even though it knew he admitted to molesting another boy in 1982. According to Zalkin, the church believed he was "repentant" of his actions and could once again be trusted with young boys.