This article documents recent trends in science funding support in Sub-Saharan Africa (SSA). We analyse these trends at the SSA regional level alongside a summary of four case studies of science funding in four Science Granting Councils (SGCs) in East Africa. Our findings support the literature on science funding in SSA regarding low levels of funding, cross-country engagement, and the need for capacity building. However, we also find there are tensions among funding and policy actors around the perceived ways in which investment in science will benefit society. We argue that the narratives and logics of science funders and their roots in ‘Republic of Science’ vs. ‘Embedded Autonomy’ rationales for SGC activity must be more transparent to enable critical engagement with the ideas being used to justify spending.