 He has coached the Australian Schoolboys, was assistant coach for Australia in 2007, and was assistant coach under Craig Bellamy of New South Wales from 2007-2010.In July 2010, Flanagan was instated as Cronulla-Sutherland head coach following Ricky Stuart's resignation with six weeks remaining in the 2010 season.As head coach of the Cronulla Sharks, Flanagan lost his first three games mostly by small margins before a breakthrough win came against premiership contenders the Sydney Roosters in round 23 of the 2010 season.