Allan Aubrey Boesak was born on Feb. 23, 1946, in Kakmas, South Africa, an isolated village in arid northwestern Cape of Good Hope. He was the seventh of eight children. His father, a teacher, and his mother, a seamstress, were both classified by the South African government as Coloured—of mixed European and African descent. With the help of scholarships Boesak was able to complete his theological studies in The Netherlands at the Calvinist theological seminary in Kempen. As a student he was inspired by the anti-Nazi German theologian Dietrich Bonhoeffer, by Martin Luther King, Jr., and by the dissident Afrikaner clergyman of the Dutch Reformed Church (DRC), the Rev. W.C. Beyers Naudé.

In 1968 Boesak was ordained in the DRC, which was closely identified with the apartheid system. Boesak was persuaded that he could be more politically effective by remaining within the DRC. Having influenced the World Alliance of Reformed Churches (with which the DRC was affiliated) to denounce apartheid as a heresy, Boesak tried to persuade the DRC to endorse this stand. His career in the church was briefly threatened when the police leaked documents alleging that he was engaging in extramarital relations with a white church worker; however, he was cleared by the church authorities. He was arrested in August 1985 when he attempted to lead a mass march to Pollsmoor Prison near Cape Town to protest against the continued detention of Nelson Mandela. He was released on bail, and his passport was later withdrawn.