 He was appointed assistant coach of NRL team Cronulla-Sutherland Sharks in 2006 and was subsequently appointed to the top position when former coach Ricky Stuart resigned on 20 July 2010.Flanagan is currently the Assistant Coach at the St. George Illawarra Dragons.Flanagan played S. G. Ball Cup, Jersey Flegg Cup and President's Cup for St. George Dragons before his NRL debut for St George in 1987.