SAT was established in 1990 as 'The Southern African AIDS Training Programme', a project of the Canadian International Development Agency (CIDA) implemented by the Canadian Public Health Association (CPHA).

In 2003, SAT became an independent regional organisation, and was re-named the 'Southern African AIDS Trust'.

SAT still delivers a large regional project for CIDA (for which CPHA remains the Canada-based executing agency). In addition SAT is developing an expanded portfolio of other work funded by a growing number of new resource provider partners. Since late 2006, SAT has been funded through a Joint Financing Arrangement (JFA) with the Canadian International Development Agency (CIDA) the Royal Netherlands Embassy (RNE) and the Swedish International Development Cooperation Agency (Sida)