The merged club won its first league premiership in 2001, and Lion Jason Akermanis won the league's highest individual honour, the Brownlow Medal. In 2002, the Lions repeated as premiers, and Lion Simon Black won the Brownlow. In 2003, the Lions became the first Grand Final participant in AFL history to have three Brownlow Medallists in its lineup, the third being 1996 honouree Michael Voss. The club went on to become the first in the VFL/AFL to win three consecutive Premierships since 1957.
This followed a breakdown in negotiations with the Fitzroy City Council over the club's request for a 40-year lease and a $400,000 loan to develop the Brunswick Street ground that was still their training headquarters.
Fitzroy won the 1978 VFL night premiership, beating Tasmania, South Melbourne and Richmond in the qualifying rounds before upsetting North Melbourne 13-18-96 to 2-8-20 at Waverley.
Fitzroy, a foundation member of the VFL/AFL, ceased to exist as a separate entity.
Fitzroy were too good for the Pivotonians though, and when they tied with Essendon in their penultimate match it left an intriguing scenario for the final week of the season.
Fitzroy ruckman Mick Grace, who had taken numerous marks, some of them spectacular, and whose long goal in the 3rd term had effectively snuffed out the last hopes of an Essendon recovery, was awarded a gold medal as the best player afield.
Fitzroy duly beat Collingwood in a semi final and Carlton in both the final and challenge final to clinch a premiership pennant to hang alongside the 1916 wooden spoon.