The Clydesdales originally played in the Queensland Cup from the competition's inception in 1996 until 2006, and were the feeder club for the Brisbane Broncos between 1999 and 2006.

The Clydesdales were the competition's big improvers as they finished in fourth place and were ultimately eliminated by the defending premiers, Norths Devils.

The following season, 2000, resulted in Toowoomba finishing third and qualifying for their second Queensland Cup grand final, beating Redcliffe 46-12 in the major semi-final.

2001 saw the Queensland Cup return to Toowoomba, as the Clydesdales finished minor premiers with just one loss and one draw all season.

Halfback Casey McGuire scored the winning try inside the last minute of the game, giving the Clydesdales a famous 28-26 victory.

The Broncos wound up the feeder club arrangement with the Clydesdales in December 2006, resulting in Toowoomba withdrawing from the Queensland Cup.

[14] Former Bulldogs NRL player Jason Alchin was named as the head coach of the Western Clydesdales for the 2023 season.