He is best known for his role as Filip "Chibs" Telford in the FX crime drama television series Sons of Anarchy (2008–2014) and its spin-off Mayans M.C.

Flanagan worked in Robert Carlyle's Raindog Theatre for three years before being cast in Braveheart (1995).

He has had roles in Face/Off (1997), The Game (1997), Sunset Strip (2000), Gladiator (2000), All About the Benjamins (2002), Charlie's Angels: Full Throttle (2003), Alien vs.

He was one of the main cast members of Sons of Anarchy, in which he plays an outlaw biker named Filip "Chibs" Telford.

In July 2018, it was announced that Flanagan was cast in one of the main roles, Alec McCullough, on the Netflix series Wu Assassins.