National Rugby League 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. Queensland won 26–18. 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. Flannery played at centre in Sydney's victory. He again played from the interchange bench for the Roosters in the
2003 NRL grand final which was lost to the
Penrith Panthers. Flannery played for Queensland in all three matches of the
2004 State of Origin series. He played for the Roosters at lock forward in their
2004 NRL grand final loss to cross-Sydney rivals,
Canterbury-Bankstown.
Super League In 2007, Flannery signed for
St. Helens on a three-and-a-half-year deal. Flannery was brought in as a direct replacement for fellow Australian
Jason Hooper who had to retire following problems with his shoulder. Flannery described himself as a hard worker and strong in defence. "I also like to add a bit to the ball playing by taking it up at first or second receiver. I also like to run good lines into holes." He commenced his
Knowsley Road career in July, 2007, after recovering from a broken leg. He played in the
2008 Super League Grand Final defeat by the
Leeds Rhinos. He played in the
2009 Super League Grand Final defeat by the
Leeds Rhinos at
Old Trafford. ==Post-playing==