Boughner was promoted from assistant coach to interim bench boss during the 2019-20 season after Peter DeBoer was relieved of his duties.
The 49-year-old guided the Sharks to a 14-20-3 record. The team dealt with some key injuries during his time behind the bench, with Erik Karlsson, Logan Couture, and Tomas Hertl all missing significant time.
Boughner previously served as the head coach of the Florida Panthers, accumulating an 80-62-22 record across two seasons.
The Sharks also named Rocky Thompson as an associate coach and John Madden as an assistant coach. Evgeni Nabokov holds his position as the club's goalie coach, and Mike Ricci will serve as an NHL developmental coach after spending the end of the 2019-20 campaign as an assistant coach.
Boughner and his staff all signed three-year deals, reports TSN's Pierre LeBrun.