After retiring as a player, Henderson was hired as an assistant coach at Duke in 1997. The Blue Devils won the ACC championship during each of his 3 seasons as an assistant coach, finishing national runner up in 1999. In 2000, Henderson was hired as head men's basketball coach at the University of Delaware. In so doing, he replaced another former Duke assistant coach,
Mike Brey, who had been selected to become the head coach at
Notre Dame. Henderson served a total of six years as head coach at Delaware. In his first season, the Blue Hens lost in the America East title game, finishing the year with a 20–10 record. After his first season, Delaware moved into a more competitive (and better funded) athletic conference, the Colonial Athletic Association. The team made the tournament semifinals the next two years, and the quarterfinals during his 4th year with the team. After consecutive losing seasons, however, Henderson was fired after the 2005–06 season. ==Scouting career==