[6] During an evening outing, he suffered a knee injury that ruled out a potential career as a football player, which Blackburn Rovers had shown interest in fostering.

Abandoning an athletic profession in 1953, he joined BOAC as a management trainee, subsequently working for the airline in Kenya, Sri Lanka, Peru, Iran, India and the UK.

In 1969, Flanagan was one of the winners of a TV playwriting competition run by the Observer newspaper and ITV's Saturday Night Theatre with "The Garbler Strategy",[7] a satire on management theory that starred Leonard Rossiter.

Flanagan was awarded a CBE in 2000 for services to communities in the United Arab Emirates and to aviation, and KBE in the 2010 Birthday Honours.

[12] Other awards include Flight International magazine's Personality of the Year, membership of the British Travel Industry Hall of Fame, Aviation Legend award by the Centre for Asia Pacific Aviation, Fellow of the Royal Aeronautical Society and Honorary Fellow (the society's highest award), Liveryman of the Guild of Air Pilots and Air Navigators, and membership of the executive committee of the World Travel and Tourism Council.