Kenneth James Ward, 40, of Modesto walked into the Church of Jesus Christ of Latter-day Saints in Visalia between Sunday services and asked for the leader of the congregation, police said.
He was directed to victim Clay Sannar, 40, who was doing administrative paperwork.
Ward later called police to say he was the shooter and let them know where they could find him, Visalia police Chief Colleen Mestas said.
Arriving officers confronted Ward and exchanged gunfire, police said. Ward was shot multiple times and pronounced dead at a hospital.
No police officers were injured.
Ward was not a member of the church and did not seem to know Sannar, church official Ralph Jordan said.
Police have not yet determined a motive.
"We have several detectives out actively investigating this so we can come up with answers, especially for the family," Mestas said. "It's just tragic."
A voicemail left Monday at Ward's home in Modesto was not immediately returned.
His brother, Mike Ward, told the Visalia Times-Delta newspaper in California on Monday that his brother was a former member of the congregation who felt wronged by a leader in 1988. He told the newspaper that his brother also was mentally ill.
Mike Ward told the Times-Delta that his brother didn't know Sannar. He says his brother had been a church member in the 1980s and was upset by a bishop then who had "shunned him to hell."
Sannar was the general manager of Soil Basics, a fertilizer company in Visalia, according to the company website.
Members of the congregation described Sannar as a well-loved family man. One of his sons is less than 6 months old.
"We're devastated," said Scott Henriksen, 47, a church member. "This is something that should not happen."