In his second game for them, he accused his Brisbane Broncos opponent Andrew Gee of biting, showing the referee a mark on his forearm.

[6] In July 2010, Flanagan was instated as Cronulla-Sutherland head coach following Ricky Stuart's resignation with six weeks remaining in the 2010 season.

[12] As head coach of the Cronulla-Sutherland 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.

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.

On 2 October, the Cronulla-Sutherland Sharks recorded a 14–12 victory over the Melbourne Storm, making Flanagan their first coach to win a premiership.

[17] He joined his junior club the St. George Illawarra Dragons as an assistant coach to Paul McGregor beginning in the 2020 NRL season.

[22] In October 2022, Flanagan joined the Manly Warringah Sea Eagles as an assistant coach to Anthony Seibold ahead of the 2023 NRL season.

[23] On 14 June 2023, Flanagan signed a three-year contract to become the head coach of the St. George Illawarra Dragons starting in 2024.

[24] In round 1 of the 2024 NRL season, Flanagan's reign at St. George Illawarra got off to the best possible start as the club recorded an upset 28-4 victory over the Gold Coast.