Shortly after the Balkan Wars, his family fled Kavala, in oder to avoid the Bulgarian Occupation of the city.

Between 1951 and 1961 he taught music at an Athens high school and from 1953 he was professor of counterpoint and composition at the Hellenic Conservatory.

[1][2] Papaioannou played a pivotal role in the inception of the festivals of Contemporary music which were financially backed by various institutions, including the Greek Tourist Organisation and several foreign entities.

[2] Papaioannou was the first musician to systematically teach atonal, 12-note and serial techniques before 1970.

His compositional career falls into five main phases: Early Impressionist (1932–8), National School (1939–43), Hindemithian neo-classicism combined with elements of Byzantine music (1944–52), 12-note period (1953–1966) and the last period (1966–89) in which he developed an entirely personal technique.