In Chicago, Flynn acted with the
Goodman and
Steppenwolf theaters. He was nominated for a
Joseph Jefferson Award (Actor in a Principal Role, for
The Ballad of the Sad Cafe, 1986). He also performed at the
Improv Olympic and the
Second City Comedy Troupe. In 1998, he founded the
improv team Beer Shark Mice with
David Koechner, which was still active as of 2015. Although his role on
Scrubs had been to that point the most visible, he had other small roles in a variety of different TV shows and movies, including ''
That '70s Show, Baby's Day Out, CSI, My Boys, Seinfeld, and Smallville''. In
The Fugitive, he plays a
Chicago police officer who is killed by the one-armed man, Frederick Sykes while he is fighting Dr. Richard Kimble. This role was used in a subplot of the
Scrubs episode "
My Friend the Doctor" when J.D. notices Flynn's character in the film and believes that Flynn's Janitor character is the actor in the film. In 2008, Flynn worked with
Harrison Ford again, playing a suspicious law enforcement official as FBI agent Smith in
Indiana Jones and the Kingdom of the Crystal Skull. Flynn had a minor role in
Mean Girls as the father of
Lindsay Lohan's character. He then played the part of an anonymous police officer in
Anchorman: The Legend of Ron Burgundy; this scene was cut out of the final version of the film, though it can be viewed in the straight-to-DVD spin-off film
Wake Up, Ron Burgundy: The Lost Movie, and in the deleted scenes of the
Anchorman DVD. He had a minor role in
Major League as a
longshoreman and fan of the
Cleveland Indians. Flynn had a role on
Phil Hendrie's animated pilot that was not picked up by
FOX. He was also first baseman Stan Okie in the movie
Rookie of the Year. Flynn appeared in an episode of
The Drew Carey Show, playing the fake husband of future
Scrubs co-star
Christa Miller. He appeared in an episode of
Seinfeld, playing a police officer.
Scrubs For
Scrubs, Flynn auditioned for the role of Dr. Cox but was given the role of
Janitor, instead. He was originally only cast for the first episode ("
My First Day"), but he became a regular, playing a character known only as the Janitor, who devotes much of his energy to menacing young
Dr. John "J.D." Dorian. His name is not revealed in the series until the season 8 finale when, upon J.D.'s first time asking about it, he simply says his name is Glenn Matthews. This is also speculated to be false for two reasons: first after J.D. leaves the shot, an orderly addresses the Janitor as "Tommy"; and second, while watching
The Fugitive with Carla and Danni (Dr. Cox's sister-in-law, played by
Tara Reid) in the season 3 episode 'My Friend The Doctor', J.D. notices the real-life Flynn's character in the train scene. When the Janitor confirms he was in the movie at the end of the episode, some fans speculated the Janitor's name in
Scrubs is
Neil Flynn, but this was dismissed by Flynn in an interview. Flynn was a series regular with
Scrubs through the first eight seasons. When
Scrubs was canceled by NBC and subsequently picked up by ABC, he signed a second position one-year deal for
Scrubs season 9, which would have allowed him to continue on
Scrubs if his pilot
The Middle was not picked up.
The Middle Flynn played the supporting role of lower-class dad Mike Heck on
ABC's
The Middle (2009–2018). The character had three children and worked at the Orson Limestone Quarry in rural central Indiana. For his work on
The Middle, Flynn was nominated for
Best Supporting Actor in a Comedy Series at the
6th Critics' Choice Television Awards.
Voice-over work Flynn has also done
voice acting for the animated series
Buzz Lightyear of Star Command, though he is better known for voicing the popular characters Skidd McMarx and the Plumber in the first three
Ratchet & Clank games for the
PlayStation 2. He also made 2 guest appearances in
Kim Possible. Flynn voiced the character Max Flush on the FOX TV show ''
Bob's Burgers'' in the episode "
O.T.: The Outside Toilet". As of 2015, he was providing the voice of Chuck, the foster father of the title character in the
DC Comics animated web series
Vixen. ==Honors and awards==