SSAJRP aims to strengthen existing research partnerships, aid the formation of new scientific networks and support knowledge transfer and innovation in Switzerland and South Africa. The programme's funding instruments have been implemented to support both established researchers and young early career scientists. Furthermore, its innovation focused entrepreneur programme brings together young entrepreneurs from Switzerland and South Africa with the aim of nurturing an innovative spirit and of creating business networks across continents.

On the Swiss side, SSAJRP is administrated by the State Secretariat for Education, Research and Innovation (SERI). The University of Basel, as the Swiss Leading House for South Africa, and the Swiss Tropical and Public Health Institute, as the Associated Leading House, jointly assume coordination and management responsibilities.