At the 2001 Australian Championships, Harrison won gold and silver respectively in the 200-metre and 100-metre breaststroke to qualify for the 2001 World Aquatics Championships in Fukuoka, Japan. He came sixth and 20th in the 200-metre and 100-metre respectively, despite setting an Australian record in the 200-metre event. He combined with Welsh, Huegill and Ian Thorpe to win gold in the 4×100-metre medley relay. Harrison had a poor year in 2002, managing only seventh in the 200-metre breaststroke at the 2002 Commonwealth Games in Manchester, and being dropped for the 100-metre event and the medley relay. He won gold and silver in the 100-metre and 200-metre breaststroke at the 2003 Australian Championships, but continued to decline, finishing outside the top twenty in both events at the 2001 World Aquatics Championships in Barcelona, Spain. At the 2004 Summer Olympics, Harrison was eliminated in the heats of the 200-metre breaststroke. He retired after the Games. After retirement he began swimming recreationally with Ginninderra Marlins.