Boughner spent the past two seasons as coach of the Florida Panthers and was a Sharks assistant for two seasons from 2015-17.
"I'm extremely excited that Bob has chosen to rejoin our staff in San Jose," Sharks coach Peter DeBoer said. "He and I have known each other for more than 20 years and we're very familiar with all the intangibles that he brings to our team."
Boughner was 80-62-22 with the Panthers and did not make the Stanley Cup Playoffs in either season. He was fired April 7 after Florida (36-32-14) finished 12 points behind the Columbus Blue Jackets for the second wild card into the playoffs from the Eastern Conference this season.
"Bob already has strong relationships with many of our key players and we expect that he will reintegrate himself into our organization seamlessly," Sharks general manager Doug Wilson said.
Boughner played 630 games as a defenseman with the Colorado Avalanche, Carolina Hurricanes, Calgary Flames, Pittsburgh Penguins, Nashville Predators and Buffalo Sabres.
Rob Zettler, who replaced Boughner as a Sharks assistant in 2017, will not return next season.
