The club's origins are borne out of the South West Queensland Junior Premier League representative Program, an elite development based program for talented SWQ Junior players in the U12-U20 age groups.
This program commenced in 2007 for the beginning of the 2008 season and was administered by the South West Queensland Football Zone. A number of these representative players moved onto the QAS (Queensland Academy of sport) and various A-League Youth Teams.
In 2012 the FFA introduced and formed the National Premiers Leagues throughout Australia as a second-tier level to underpin the 'A' league and applications were invited to nominate for the new competition.
A new club named South West Queensland Thunder Football Club Ltd was formed and established in 2012 and was granted an invitational license to participate in the 2013 National Premier Leagues Queensland season with Junior Boys through to an U20 Team.
The Youth (U20) Men’s Team finished a credible fourth in the inaugural season progressing to the grand final, and the club was subsequently granted a full PS4 National Premier Leagues license for the 2014 season.