Barker was appointed coach of Bafana BafANA in 1994, three years after South Africa's apartheid policy was abolished. He led his team to the title of African champion two years later, in 1996, beating Tunisia in the final of the CAN in Johannesburg (2-0), in the presence of South African President Nelson Mandela.

Still under his leadership, the South African team then qualified for the 1998 World Cup in France, in which he did not participate, being sacked a few months before the competition.