Kirby found his way back into the national team at the 1997 FINA World Short Course Swimming Championships in Gothenburg, Sweden. Although he missed selection for the 1998 World Aquatics Championships in his home town, he bounced back to qualify for the 1998 Commonwealth Games in Kuala Lumpur, where he won a silver medal in the 200m butterfly. At the 1999 Pan Pacific Championships in Sydney, he was a member of the 4 × 200 m freestyle relay team (along with Michael Klim, Ian Thorpe and Grant Hackett) that lowered the world record, at the time, to 7m 8.79s. Training at the Australian Institute of Sport, he earned an Olympic berth the following year, anchoring the Australian 4 × 200 m relay team of Thorpe, Klim and Todd Pearson to another world record of 7m 7.05s.