From its inception CREST has been involved in offering a range of graduate programmes in the broad field of social research methods, as well as Science and Technology Studies (STS). CREST launched two dedicated postgraduate programmes in STS in 1997 (M.Phil in STS) and in 1998 (PhD in STS). The programmes introduce students to the social, political, economic, epistemological, historical and ethical dimension of science as a complex human system. They involve teaching of and student participation in ten specialised modules in STS, as well as supervised research in STS. The M.Phil and PhD in Science and Technology Studies is the only specialised postgraduate programme in the methodology of STS in South Africa. It has attracted students from across the continent and from various disciplines.

In addition to the programmes in STS, CREST developed, and introduced, a Masters and Doctoral Programme in Social Science Methods  in 1997. (The programmes are no longer offered by CREST but by the Department of Sociology and Social Anthropology.) These programmes offered two one week modules on Programme Evaluation Methods (one of the first programmes to do so in South Africa). The interest in the these modules led to the introduction of  a dedicated graduate programme in Monitoring and Evaluation (M&E) by CREST in 2006 – the Postgraduate Diploma in Monitoring and Evaluation Methods. The Diploma was first offered in 2006 with generous seed funding by the Carnegie Corporation of New York. CREST introduced a M.Phil in Monitoring and Evaluation, and a PhD in Evaluation Studies in 2012. To date more than 800 students have graduated from these programmes.

In 2012, CREST introduced a focus on Research Uptake and Utilisation within its M.Phil in STS programme. This generated high levels of interest across the continent. An online course in Science Communication was introduced in 2015, with the financial support of DFiD. CREST introduced two specialisations into its M.Phil programme: one in Research Management and Evaluation, and a second in Science and Public Engagement in 2017. The specialisations were developed by the academic staff of CREST to meet the increasing demand for training in research management, research evaluation, research uptake and societal impact, science engagement, scientific communication, and on topics in the area of bibliometrics and scientometrics. In addition, students are encouraged to choose a research topic that are aligned with the research streams of CREST. The latest academic degree in STS, introduced by CREST, is the Postgraduate Diploma in Research Management and Administration. The programme was developed in, and for Africa, through an Erasmus+ programme funded project entitled StoRM.