Football Federation Australia hoped to build on the success of the first season and on the interest generated by the Socceroos competing in the 2006 FIFA World Cup.

The Pre-Season Cup was used to enhance the A-League's profiles by playing pre-season games in regional centres including the Gold Coast, Sunshine Coast, Toowoomba, Launceston, Canberra, Wollongong, Port Macquarie, Orange and Tamworth.

The league season took a triple round-robin format, and took place over 21 rounds between 25 August 2006 and 21 January 2007.

The Asian Football Confederation announced on 21 November 2006 that Adelaide United and Sydney FC would represent Australia in the 2007 AFC Champions League.

Despite an appeal by the Football Federation Australia, it was determined that the 2005–06 A-League premiers and champions would qualify and not those from the current season.