The Mariners were formed during 2004 for the foundation of the A-League in 2005–06. Despite being considered one of the smaller franchises in the A-League they have qualified for a disproportionate number of finals.

The Mariners had a successful first season, winning the 2005 Pre-Season Cup and losing in the A-League grand final to Sydney FC. The Mariners then made the final of the Pre-Season Cup again in 2006, however they lost to Adelaide United. The Mariners came sixth in the 2006-07 A-League competition, and failed to qualify for the finals series. The Mariners claimed their first A-League premiership in 2007-08 by goal difference, holding on after starting the season strongly. The Mariners defeated derby rivals Newcastle Jets in the major semi-final to qualify for the Grand Final, which they lost to the Jets 1-0.