Brendan Flanagan first started training MMA for self defence back in 1998, aged 13 when he joined the British Combat Association (BCA). During this time, he was mentored by the famous self defence instructors Jeff Thompson and Peter Consterdine. 

 
He made his pro MMA debut in 2007 when he fought and beat Steve Baggaley. This was followed by another victory over Dion Oaks later that year before losing his next two fights, firstly against Nick Osipczak and then against Edgelson Lua. He got back on winning terms shortly after by beating Chris Thompson. This however would be his last victory for almost four years in which time he lost to David Round on a KnuckleUp MMA card in 2009 and Hayden Critchfield in 2010. He stepped back into the cage in 2012 and beat Steve McDonald in the first of his two fights against him. He rematched Steve McDonald again in his next fight two years later after McDonald stepped in after Flanagan's original fight against Dave Rintoul on Too Much Talent: Fight Night 5 fell through. Flanagan also won the rematch, this time via a side choke after 53 seconds of the first round, leaving few to doubt who the better of the two fighters were. His cancelled fight against Dave Rintoul was rescheduled in 2015 in which he was beaten. This proved to be his last fight as he retired from MMA in 2015 with a pro MMA record of 5-5-0. 

 
In April 2013, between his two fights with Steve McDonald, he set up his own MMA gym under the name "BODYZONE COMBAT" after being asked to collaborate with "BODYZONE GYM" in Bracknell who wanted to expand the type of training they offered. He relaunched it as "The BAT CAVE Gym" in 2014 and they are still closely linked to "BODYZONE GYM". As off January 2022, he is still the head coach at "The BAT CAVE Gym".

 
During his career, he has also competed on the European BJJ circuit and is affiliated with the Carlson Gracie BJJ Team. He currently holds a 3rd degree black belt in BJJ.