He was born in Retreat, Western Cape, in 1943, the first child in a musical family. He played piano at the age of seven, and later clarinet and trumpet. In his mid-teens he learned the alto and tenor saxophone. He cites John Coltrane, local saxophonist "Cups & Saucers", pianist Merton Barrow, as well as bassist Midge Pike as major influences.
Mankunku chose to remain in his native Cape Town during apartheid. This meant that he was subjected to the Separate Amenities Act and similar apartheid legislation. A classic tale tells of his performance with an all-white big band in the Cape Town City Hall in 1964, where, because a mixed-race band was unlawful, he was forced to play behind a curtain so as to remain out of sight.
In 1968 he recorded the famous blockbuster "Yakhal' Inkomo", with Early Mabuza, Agrippa Magwaza and Lionel Pillay