Prior to the 2006 season, the VFL–AFL reserves affiliation which had existed for the previous three seasons between North Melbourne and Port Melbourne was terminated. In its place, North Melbourne arranged to be affiliated with both North Ballarat and Tasmania, with half of its reserves players allocated to each team. Port Melbourne continued as a stand-alone senior team in the competition.[1]
As a result, the competition stayed constant at thirteen teams: ten VFL–AFL affiliations, one AFL reserves team (Geelong) and two stand-alone VFL teams (Port Melbourne and Frankston).
Box Hill won the reserves premiership. Box Hill 10.11 (71) defeated Williamstown 8.11 (59) in the Grand Final, held as a curtain-raiser to the Seniors Grand Final on 24 September.[7]
Commencing this season, a two year rule trial was conducted throughout the VFL premiership season on behalf of the AFL, under which a backwards kick to a team-mate which was caught in the defensive half of the ground would be called play-on instead of a mark; a line was painted across the centre of the field to accommodate.[8]