"After an exhaustive search, we are pleased to welcome Bob as the new head coach of the Panthers," general manager Dale Tallon said in a statement. "He sees the game in a modern way and is eager to work with our young players.
"During the interview process, Bob blew us away with his preparation, his passion, knowledge and dedication to the game. We believe that he is the right leader to get our team back to competing towards our goal of winning the Stanley Cup."
Boughner, 46, has never been a head coach at the NHL level. He previously coached the Windsor Spitfires of the OHL for two different stints (2006-2010, 2011-2015), winning two championships and a pair of Memorial Cups.
San Jose Sharks coach Peter DeBoer tapped him as an assistant each of the last two seasons. The Sharks were a Stanley Cup runner-up in 2015-16 and lost in the first round this postseason.
Boughner previously played 10 NHL seasons for six franchises before retiring from the game following the 2005-06 season.
The Panthers are in the midst of a franchise retooling after a messy 2015-16 season. Boughner will be replacing Tom Rowe, who took over as head coach last November after the team fired Gerard Gallant. Florida has made the playoffs just twice in the last 16 seasons.