In 1986 Flynn appeared in the LWT television film London's Burning as firefighter Kenny "Rambo" Baines. When the film spawned a series of the same name in 1988, he was the only member of the main cast who was unable to reprise his role (aside from Gary McDonald, whose own character, Andreas "Ethnic" Lewis, was killed off in the film) due to previous commitments. Also in 1986 he played a minor role as the soldier "Franny" in "The Monocled Mutineer".In 1988 he played the character Freddie in the ITV drama; The Fear which was about the London underworld. He appeared as D.S Eddie Hargreaves for six episodes of the police drama Between The Lines (1992).
Having taken childhood holidays in Pembrokeshire, Wales with his family, as a then follower of Ratu Bagus, Flynn and some friends moved to a Georgian house there in the late 1990s, where he still lives to this day.
Soldier Soldier ended in 1997. Flynn went on to star as Eddie Wallis (alongside singing partner Robson Green) in the comedy-drama Ain't Misbehavin' (1997), and was the star of the short-lived police show Badger in 1999. He played Bobby Charlton in the 1999 film Best. On stage, he played Tommy Cooper in Jus' Like That, a tribute to the comic Magician written by John Fisher and directed by Simon Callow.
Having semi-retired from acting and moved to Pembrokeshire, in 2007 Flynn directed and starred in the low budget film, Rude Tales. The film was split into a series of short stories, all centred around the lead character, Jerome Rude, played by Flynn. The film was screened at a small number of independent cinemas in the Pembrokeshire area.
After almost 10 years away from acting, in July 2010 it was confirmed that Flynn would be playing the role of Bronn in the HBO television series Game of Thrones, based on the A Song of Ice and Fire novels of George R.R. Martin.
Flynn was reportedly linked to Game of Thrones co-star Lena Headey; however, the relationship ended on bad terms some time before March 2014, resulting in the couple being kept apart on-set.
In 2016, he appeared in "Shut Up and Dance", an episode of the anthology series Black Mirror.
In July 2017, Flynn recorded a Sleep Story for meditation and mindfulness app, Calm. In this recording, he reads an original fiction story called "A Magical Winter Night". Sleep Stories, launched by Calm in December 2016, are bedtime stories for adults.
