Elected in November 2009, Mueller oversaw a tumultuous period when cycling grew in Australia but it's image suffered in the wake of the high-profile doping case involving American Lance Armstrong.
While the American was stripped of his record seven Tour de France titles and handed a life ban last year, Australian duo Matt White and Stephen Hodge also admitted to doping before they retired from cycling and quit their CA posts.
"It's been an honour to lead Cycling Australia through many highs and lows," Mueller was quoted as saying in a CA statement.
"In recent times the position has grown into almost a full time role, which I can simply no longer manage.
"Given the challenges the sport is currently facing the timing is right to hand the reins over to a new leader with a different skill-set to enable the sport to realise its enormous commercial potential," added Mueller, who will stay on in the post until the end of September to ensure a smooth transition.