Indianapolis, Indiana, she won silver the 400-metre individual medley. At the 2003–04 FINA Swimming World Cup event in Melbourne, she won the 400-metre individual medley. At the Australian Short Course Championships in Hobart she took the silver medal in both the 200 and the 400-metre individual medley. In July, at the 2003 FINA World Championships, she improved by one position on her result in 2001, finishing eighth in 400-metre individual medley. At the 2004 Australian Championships and Olympic Selection Trails she won the 400 metre individual medley event for the sixth consecutive year and in process broke the broke Australian record in a time of 4 mins 40.71 sec. She also finished fourth in the 800 metre freestyle and seventh in the 200 metre individual medley. At the Olympics itself, she failed to make the final of 400 metre individual medley, finishing 19th overall. In March 2005, at the Australian Championships and World Championships Selection Trails, after qualifying fastest in the heats of 400-metre individual medley, she had to withdraw from the final meaning she was unable qualify for the 2005 FINA World Championships in Montreal, Canada. Lara Carroll was crowned the Australian Champion in the event, the first time in seven years that someone other than Reilly had won the event. In August, at the Australian Short Course Championships and World Short Course Championships Selection Trails in Melbourne, she finished behind Carroll to take silver in 400-metre individual medley. However, silver wasn't enough to make the squad for 2006 FINA Short Course World Championships in Shanghai, China. In February 2006, at the Australian Championships and Commonwealth Games Selection Trails, Reilly claimed back her 400-metre individual medley national crown from Lara Carroll and in process earned the chance to defend her Commonwealth title. She also finished fourth in 200-metre individual medley and seventh in 200-metre breaststroke events. In March at the 2006 Commonwealth Games in Melbourne, Australia, she was unable to retain her title as 400-metre individual medley Commonwealth Champion, touching the wall after Stephanie Rice and Rebecca Cooke. In August at the 2006 Pan Pacific Swimming Championships in Victoria, British Columbia, Canada, she failed to the make the final of the 400-metre individual medley finishing 12th overall. In December 2006, at the 2007 Australian Championships and World Championships Selection Trails in Brisbane, Reilly took out, for the eighth time in nine years, the 400 metre individual medley event and