This chapter explores the main achievements and remaining challenges in the governance of the South African science, technology, and innovation (STI) system. While reflecting on the inherited features from the apartheid period, it focuses on the period between the two White Papers in 1996 and 2019. The chapter discusses the main shifts in policy emphasis (intents) of these two policy/institutional developments and connects them to the STI system performance and its measurement. It shows that the drastic shift in policy orientation towards addressing social imperatives and the quantitative improvements in the STI outputs since 1994, have not materialized in a radical transformation of the economy or the social relations inherited from apartheid. The chapter argues that the assessment of the STI system needs to be expanded through an evolutionary lens in order to activate the needed systemic transformations.