In 1994, the Government of Flanders opted for South Africa to become a priority partner within Flemish foreign policy. Flemish cooperation initially focused on assistance towards the building of a new, democratic South Africa, but this was subsequently extended to include development cooperation, culture, science and innovation, economy and trade, youth policy and education. On 28 October 1996 the Treaty between the Government of Flanders and the Government of the Republic of South Africa on cooperation in the fields of education, art, culture, science, technology and sport was signed, and later extended in 2002 to include all Flemish competences. Various actors became involved with this cooperation, from Flemish ministers and government departments, to scientific and tertiary institutions, non-governmental organisations, businesses and private entities.

A Flemish Trade Office in South Africa was opened in 1994. On 14 February 1999, the first General Representative of the Government of Flanders took up his function in Pretoria, serving as first point of contact between governments, government departments and other actors in Flanders and South Africa. The remit of the General Representation includes South Africa, Mozambique, Malawi, Namibia, Botswana, Swaziland and Lesotho.