Born in Cowra, New South Wales, Flannery's family moved to the Sunshine Coast, Queensland when he was 10, where he played his junior rugby league for the Kawana Dolphins.

[6] Flannery made his National Rugby League début for the Sydney Roosters in Round 14 of the 2000 NRL season against the Wests Tigers at Campbelltown Stadium on 7 May.

He was first selected to play for Queensland in Game II of the 2002 State of Origin series at ANZ Stadium in Brisbane on 5 June.

Flannery played for the Roosters from the interchange bench in their 2002 NRL grand final victory over the New Zealand Warriors, scoring a try.

Having won the 2002 NRL Premiership, the Roosters traveled to England to play the 2003 World Club Challenge against Super League champions, St. Helens.