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. From 1989 to 1991, he played for Western Suburbs Magpies then moved to Parramatta Eels from 1992 to 1994. He retired from playing football following a knee injury and was engaged to coach the Parramatta SG Ball team in 1997.
Coaching career
He had spent the 1997 season in Super League as Stuart Raper's assistant at Castleford Tigers before he was assistant coach for the Sydney Roosters for two years under Ricky Stuart. 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. The Sharks won 18-12. The Sharks won one more game in the 2010 season, against the Gold Coast Titans. In the 2012 NRL season, Flanagan coached Cronulla to finish 7th on the ladder. Flanagan built a reputation for signing key players to the club. Having signed Todd Carney the previous year, Flanagan secured the purchases of Beau Ryan and Chris Heighington from the West Tigers, Michael Gordon and Luke Lewis from the Panthers and Jonathon Wright from the Bulldogs. In 2013, following a year-long investigation into the Sharks' supplements program carried out during the 2011 NRL season, Flanagan was suspended from his role for a period of 12 months. In the 2016 NRL season he guided Cronulla to a top four finish. They would travel to Canberra in the first week of the 2016 Finals and record a 16-14 victory thus earning a preliminary final at Allianz Stadium. The Cronulla Sharks would win this preliminary final against the 2015 premiers, the North Queensland Cowboys, by 32-20 thus earning a place in the 2016 Grand Final. On 2 October, the Cronulla Sharks would record a 14-12 victory over the Melbourne Storm and win the Premiership becoming the first head coach of the Cronulla Sharks to win a premiership. In the 2017 NRL season he guided Cronulla to the finals. In week one, Cronulla played against North Queensland in the elimination final. Cronulla went to be upset 15-14. In 2018, Flanagan took Cronulla to a top four finish. Cronulla lost their week one final match against Eastern Suburbs before defeating Penrith the following week 21-20. In the preliminary final, Cronulla were defeated by Melbourne 22-6. On 19 December 2018, Flanagan was de-registered as a coach indefinitely for failing to adhere to the conditions of his suspension in 2014. The NRL integrity unit had found that Flanagan had sent more than fifty emails exchanged between Flanagan, club management and the football department which was strictly against the conditions of his suspension which included that Flanagan was to have no contact or involvement with the club during his ban. The NRL also fined Cronulla $800,000 as punishment. On 20 September 2019, it was announced that Flanagan was allowed to return to the NRL but under strict conditions. It was reported that Flanagan was still unable to hold a head coaching role at any club until 2022 but was allowed to return as an assistant coach. On 27 November, 2019, it was announced that Flanagan had joined his junior club the St. George Illawarra Dragons as an assistant coach to Paul McGregor beginning in the 2020 NRL season. Flanagan's role is specifically focused on defence. Flanagan was the most important of one of 8 coaching changes at the Dragons following a dismal 2019.
