Whisenhunt was fired from his role as head coach at the Arizona Cardinals at the end of the regular season, after the side finished bottom of the NFC West.
The Chargers' new head coach Mike McCoy told the team's website: "Ken has a lot of experience and has had much success in the NFL in both Arizona and Pittsburgh.
"He has a very creative mind and will be a great asset for me and our team. I look forward to working with him."
San Diego sacked their coach and general manager at the end of the season, having missed out on a place in the playoffs.