In 2005, Jeter was hired to replace Bruce Pearl at Milwaukee, who led the Panthers to the Sweet 16 in the previous season during the 2005 NCAA Tournament. Jeter would guide the Panthers to another Horizon League conference and tournament title and a first-round win over Oklahoma in the 2006 NCAA Tournament. During the next 10 seasons, Jeter would help the Panthers to another Horizon League regular season title and a berth in the 2011 NIT as well as a 2012 CBI appearance and another Horizon League conference tournament title for a spot in the 2014 NCAA Tournament. At the conclusion of the 2015–16 season, Jeter was fired by Milwaukee by Athletic Director Amanda Braun.