Early years

O'Flanagan attended Synge Street CBS,^[2] Dublin where the main sport was Gaelic football and he was subsequently included on the minor Dublin county panel. The panel also included Johnny Carey and together they also played soccer with Home Farm. When the Gaelic Athletic Association found out, O'Flanagan, but not Carey was dropped from the panel. He continued to play soccer and joined Bohemian, making his first team debut at 16. In the summer of 1937 he played for an Ireland junior team against a Birmingham FA XI at West Bromwich and scored twice in a 4–3 win. His performance resulted in offers from Liverpool, Aston Villa and Manchester United, but his parents insisted that he complete his education.

University years

In 1937 O'Flanagan began studying medicine at University College Dublin and it was while there that he developed into an all-round sportsman. He continued to play soccer for Bohemian and on 7 November 1937, aged 18, he scored on his senior debut for Ireland against Norway, in a qualifier for the 1938 FIFA World Cup. In 1945 he also captained Bohs as they won the Dublin and Belfast Intercity Cup, beating Belfast Celtic 3–2 on aggregate in the final.

It was while at UCD that O'Flanagan first took up rugby union, playing for the university team, and in 1942 he received his first call up to the Ireland squad. O'Flanagan also emerged as a prominent athlete and was Irish long jump champion in 1939 and the 60 yards and 100 yards champion in 1941. In 1941 he tied with David Guiney for the long jump title, but with only one gold medal available, he insisted his rival accept it as he already had one. Only the Second World War prevented O'Flanagan representing Ireland at a third sport.

London years

After qualifying as a doctor from UCD in 1945, O'Flanagan was offered a position as a junior GP in Ruislip, Middlesex. He maintained his interest in sport, however, playing soccer for Arsenal and rugby union for London Irish. Despite being good enough to play soccer as a professional, he remained an amateur so he could continue to play rugby union. In his debut season with Arsenal, 1945–46, he scored 11 goals in 18 Football League South appearances, finishing as the club's top scorer; he also played a further two games for Arsenal in the FA Cup in a two-legged tie against West Ham United that Arsenal lost 6–1 on aggregate.

During the 1946–47 season he made 14 First Division appearances and scored 3 goals. He made his first-class league debut^[3] against Blackburn Rovers on 4 September 1946. His last appearance for the Arsenal senior team came on 28 December 1946 against Wolves. He continued to play for Arsenal Reserves until 1948 and later played for both Barnet and Brentford before his increasing medical commitments and an ankle injury, forced him to retire as a sportsman in 1949. However O'Flanagan, who was now a specialist in sports medicine, had already embarked on his next career. A chance encounter with FA chairman Stanley Rous led to his appointment to the British Olympic Medical Commission and to him becoming team doctor for Great Britain at the 1948 Summer Olympics.

Soccer international

When O'Flanagan began his international soccer career in 1937 there were, in effect, two Ireland teams, chosen by two rival associations. Both associations, the Northern Ireland – based IFA and the Irish Free State – based FAI claimed jurisdiction over the whole of Ireland and selected players from the whole island. As a result, several notable Irish players from this era, including O'Flanagan, played for both teams.

Between 1937 and 1947 O'Flanagan made 10 appearances and scored 3 goals for the FAI XI. He won 7 of these caps while playing for Bohemian and made his international debut against Norway on 7 November 1937, in a qualifier for the 1938 FIFA World Cup. O'Flanagan scored in the 3–3 draw. His teammates on the day included fellow debutant, Johnny Carey and Jimmy Dunne. The highlight of his international career came when he scored twice in a 2–2 away draw against Hungary on 18 May 1939. With Hungary 1–0 up at half-time, O'Flanagan turned the game around with two magnificent goals in the 52nd and 77th minutes. He scored the first with his left foot from twenty five yards and the second with his right foot from a similar distance. Only a very late goal denied the FAI XI victory.

In 1939 O'Flanagan also played twice for the League of Ireland XI, helping them to 2–1 victories against an Irish League XI and a Scottish League XI.^[4] He won his last three caps for the FAI XI while at Arsenal. These included the game against England on 30 September 1946 when his teammates included his brother, Mick O'Flanagan. He made his final appearance for the FAI XI on 4 May 1947 in 2–0 defeat against Portugal. In 1946, while at Arsenal, O'Flanagan also played in two Victory internationals for the IFA XI. On 2 February at Windsor Park he played for the IFA XI in a 3–2 defeat to Scotland. Then on 4 May he helped the IFA XI defeat Wales 1–0 at Ninian Park.

Rugby international

In 1942, while playing for UCD, O'Flanagan played for an Ireland XV against a British Army XV at Ravenhill. In 1946, while with London Irish, he played on the wing in an unofficial international against France. In 1947 he won his only official cap in a Test against Australia, a 16–3 defeat at Lansdowne Road.