Flynn began his working life as a school teacher, but in 1903 decided to train as a Presbyterian minister. He entered training in divinity at Melbourne University in 1907 and graduated in 1910. At various times throughout his training Flynn worked remote areas of Victoria as a student lay pastor and he also published Bushman's Companion, a book of general information for those living in the bush. Flynn was ordained in January 1911 and volunteered for a post at the Smith of Dunesk Mission at Beltana in the northern Flinders Ranges, South Australia.

In 1912, Flynn was commissioned to make a survey of the Northern Territory and report to the Presbyterian General Assembly on the needs of the indigenous peoples and European settlers. As a result of his reports, Flynn was appointed superintendent of the Presbyterian Church's Australian Inland Mission (AIM). The parish of the AIM was vast and Flynn sent a team of 'patrol padres' on camel or horseback to minister to remote communities throughout the parish. AIM also established a network of hostels and hospitals to service remote communities.

In 1928 Flynn established the AIM Aerial Medical Service at Cloncurry, Queensland. The Service sent doctors by aircraft to the scene of medical emergencies in remote parts of Australia. The one main drawback of Flynn's plan was that there was often no telephone or radio link between the remote homesteads and the AIM Aerial Medical Service base and many had to travel a long way to be able to contact the service. The following year a pedal wireless, invented by South Australian Alf Traeger, was installed at the AIM Aerial Medical Service base and the radio network grew from there. The AIM Aerial Medical Service radio network not only helped those living in remote areas in medical emergencies, but being able to contact one another helped with feelings of isolation and loneliness and was also vital part of the establishment of the School of the Air in Alice Springs in 1951. The AIM Aerial Medical Service was relinquished by the Presbyterian Church in 1934 and established as the Australian Aerial Medical Service with government assistance. Its name changed to the Flying Doctor Service of Australia in 1942 and in 1955 the Royal Flying Doctor Service of Australia. By 1950 bases were established at Wyndham, Port Hedland, Kalgoorlie, Broken Hill, Alice Springs, Charleville and Meekatharra.

Flynn was made an Officer of the Order of the British Empire in 1932 in recognition of his work bettering the lives of those living in the Australian outback. He served as the Moderator-General of the Presbyterian Church. The John Flynn Memorial Church was opened at Alice Springs in 1956.

17 May 1928: The AIM Aerial Medical Service - the first aerial medical service in the world - answers its first call and attends a medical emergency at Julia Creek; the organization is to develop into the Royal Flying Doctor Service of Australia.

June 1933: Made Officer of the Order of the British Empire (OBE)

1939-1942: Moderator-General of the Presbyterian Church

Reverend John Flynn appears on the Australian $20 note.

Idriess, Ion L. Flynn of the Inland, Sydney : Angus & Robertson, 1973

Rudolph, Ivan. John Flynn : of flying doctors and frontier faith, North Blackburn, Vic. : Dove, 1996

National Archives of Australia: See Publications: Fact Sheets: Personalities: Flynn, Reverend John and the Australian Inland Mission

Reserve Bank of Australia: See Currency Notes: Notes in Circulation: $20

Royal Flying Doctor Service of Australia: See Our History: About John Flynn