[1] Although capped at Ireland Schools level while attending St Munchin's College (Limerick), and with a fine underage pedigree, Flannery had to wait patiently for his opportunities, but made the most of those that eventually came his way.
Flannery then moved to Munster, where he initially found his opportunities severely restricted by the consistent form of Frankie Sheahan, a regular Ireland international.
He did, however, make his Heineken Cup debut as a replacement against Stade Français at Thomond Park in the quarter final in April 2004, which Munster won 37–32.
Voted Man-of-the-Match on his first try-scoring Heineken Cup start against Castres, Flannery's outstanding form and ability to compete at the highest level meant that he was promptly called into the Ireland squad, and made his international debut against Romania in November 2005 where he came on as a replacement.
By January 2006, Flannery was installed as Ireland's first-choice hooker, and played his first full international game against Italy in the Six Nations Championship.
[3][4] In February 2010, Flannery was cited for "an alleged kick" on France wing Alexis Palisson during the 2010 Six Nations Championship defeat in Paris.
The opening game against the USA turned out to be Flannery's last for Ireland, as injury ruled him out of the 2012 Six Nations Championship and forced him to retire in March 2012.
[11] In July 2013, Flannery joined Premier League football team Arsenal on a work placement as a strength and conditioning coach.