Flanagan began his musical career at age 11 in 1978, drumming for the New York punk band the Stimulators alongside his aunt Denise Mercedes.

His father was a petty criminal and his mother was a memoirist, actress and prominent figure in Greenwich Village's bohemian culture, being featured in films such as Piero Heliczer's Dirt (1963) and Harry Everett Smith's Mahagonny (1980).

[4][5] On May 19, 2018, Flanagan's band was one of four classic punk/hardcore acts to play the Prudential Center in Newark, New Jersey, along with Murphy's Law, Suicidal Tendencies, and the Original Misfits.

His students included the daughter of Anthony Bourdain, who coincidentally attended NYC Stimulators concerts in the early 1980s, and was a fan of the then preteen drummer.

[11] On July 6, 2012, Flanagan was arrested for allegedly stabbing two current members of Cro-Mags, and biting one of them, backstage at the Webster Hall in New York City.

In 2018, Flanagan filed a lawsuit in federal court charging former band members John McGowan and Maxwell Jayson with trademark infringement.