Flanigan had guest roles in numerous television series including Profiler, First Monday, and Sisters, until he got his breakthrough with his role on Stargate Atlantis as Lt. Colonel John Sheppard.
Flanigan hatte Gastrollen in zahlreichen TV Serien wie zum Beispiel Profiler, First Monday und Sisters, bis ihm der Durchbruch mit der Rolle des Major/Lt. Colonel John Sheppard in Stargate Atlantis gelang.