He was born in 1909 in Hobart, Tasmania, Australia. He was born to Theodore Thomson Flynn and Marelle. From 1923 to 1925 Flynn attended a private boarding school, South West London College in Barnes, London. In 1926 he came back to Australia to attend Sydney Church of England Grammar School. His formal education ended from Shore School when he was expelled on account of theft, but according to him it was because of a romantic assignation with the school’s laundress. He worked as a junior clerk with the Sydney shipping company, but was dismissed from there for pilfering petty cash. At the age of eighteen he went Papua New Guinea seeking but failing to find his fortune in tobacco planting and metal mining. For the other five years he oscillated between New Guinea and Sydney.
Flynn had married three times: In 1935 to 1942 to Lili Damita and had one son with her, Sean Flynn. Then married Nora Eddington in 1943 to 1949 and has two daughters with her, Deirdre and Rory. Lastly married Patrice Wymore in 1950 and remained married to her till his death and has one daughter with her, Arnella Roma.
In 1933, Flynn initially appeared as an apprentice actor in the Australian film 'In the Wake of the Bounty'. In the same year he decided to pursue a career in acting and shifted to Britain. Here he got a job with the Northampton Repertory Company at the Royal Theatre, also received a professional training as an actor for seven months. From here he was dismissed in 1934, after he threw a stage manager down a stairwell. After this he went to Warner Brothers’ where he had once worked as an extra. He was cast in 'Murder at Monte Carlo' as a lead and during this time he was signed by Warner Bros and emigrated to US as a contractor actor. His first Hollywood role was in 'Captain Blood' as swashbuckler that made him a sensation. Through this role he contributed to the reinvention of the action-adventure genre for the next six years. His first book was published in 1937, "Beam Ends", which was an autobiographical account of his sailing experiences around Australia during his youth. During the Spanish Civil War, in 1937 he travelled to Spain as a war correspondent.
In 1942, he became a naturalised citizen of America. The World War II had started and Flynn attempted to enlist himself in the armed services. His attempt failed as he had multiple heart problems, recurrent malaria, chronic back pain, TB and various venereal diseases. Later this image created problems for him as well as Warner Bros as he was still being cast in athletic roles.
His adventure novel, "Showdown" was published in 1946. It is estimated to having earned $184,000 (equivalent to $2,230,000 in 2015).
During the second half of 1940's the film industry was undergoing a lot of change. The context has changed to urban realism and gritty from the olden European and English history. Flynn was unable to keep pace with changing times. His frustration could be seen during his films and it took a toll on his financial and physical situation.
By 1952, his health had deteriorated to a great extent and he got hepatitis, which resulted in damaging his liver. By 1959, his financial condition had reached an all time low so much so that he had to go to Vancouver to lease out Zaca, his yacht. This was his last trip as during this visit he died of a heart attack and cirrhosis of the liver.