The move is strictly a hockey decision, according to Sportsnet's Elliotte Friedman, as the team has gone 15-16-2 in 2019-20 after reaching the Western Conference Final last spring.
DeBoer was in his fifth season behind the bench with San Jose. The Sharks made the playoffs in each of his previous four campaigns at the helm, losing to the Pittsburgh Penguins in the Stanley Cup Final during his first year with the club in 2015-16.
The 51-year-old joined San Jose after three-plus seasons with the New Jersey Devils and three campaigns with the Florida Panthers. He guided the Devils to the Cup Final in 2012.
He's the fifth NHL bench boss to lose his job in 2019-20. Three of the other four were fired, and Bill Peters resigned from his post with the Calgary Flames.
Boughner previously served as Panthers head coach from 2017 to 2019.