Neil Flynn grew up acting in school plays. He has been awarded with two Jefferson Awards for excellence in Chicago Theatre. Later on he became involved in projects on both the big and small screen.

Flynn has had roles in several features, among them The Fugitive, Magnolia, Mean Girls, Chain Reaction, and more. Flynn's role on Scrubs as The Janitor became so pivotal during the first season that his guest star position was upgraded to resident cast member. Flynn is a master at improvisation and usually makes up his lines on the spot.