The 2006 Horizon League men's basketball tournament took place at the end of the 2005–06 regular season.
Milwaukee hosted the second round and semifinals, because they were the top seed overall, as well as the final because they were the highest remaining seed.
All Horizon League schools played in the tournament.
Teams were seeded by 2005–06 Horizon League season record, with a tiebreaker system to seed teams with identical conference records.
First round games at campus sites of higher seeds Second round and semifinals hosted by the top seed.