Flatley figured prominently in Australia's 2003 Rugby World Cup campaign, going right to the final against England and scoring the penalty that took the match to extra time, then another penalty which evened the scores at 17-17 before England ultimately prevailed. He finished the tournament as the third highest point score, scoring 100 points for Australia. In April 2004, Flatley reached another milestone, becoming the youngest player ever to reach 100 caps for the Queensland Reds when he led the side out against the Sharks in Durban. Flatley prematurely retired from all forms of rugby on 16 March 2006, on medical advice as he was suffering from continued blurred vision due to a number of concussions. In 2006 he was a contestant on Australia's Celebrity Survivor.