The 2002 season saw Geylang United finish third in both the S.League and Singapore Cup. They came close to winning their third S.League title and first Singapore Cup in 2003, only to finish runners-up to Home United for both competitions. As runners-up, they qualified to play in the AFC Cup 2004 due to Home United's double. Their debut in the AFC Cup 2004 was an impressive one. Despite losing their opening match, they managed to stay unbeaten for their next five games in the group stage. They went on to qualify for the quarter-finals, beating Perak FA before losing to Al-Wahda in the semi-final.