He won the 2014 Super League Grand Final with Saints, and spent time on loan from the club at the Rochdale Hornets in the Championship.

After some impressive performances in the reserves Flanagan made his Wigan début from the bench during the second half of a 22–16 defeat by the Crusaders RL at Brewery Field.

[7][8] He made more appearances for Wigan putting in some very impressive performances, most noticeably for his defensive effort in the derby loss away at St Helens.

St Helens reached the 2014 Super League Grand Final, and Flanagan was selected to play at scrum-half in their 14–6 victory over the Wigan Warriors at Old Trafford.

[10][11][12][13][14] Flanagan left St Helens at the end of the 2015 season to join Salford, where he was reunited with his former Wests Tigers coach Tim Sheens.