Building and strengthening transformative science (and research, technology and innovation, collectively, STI) systems in sub-Saharan Africa (SSA) is as much a political and economic challenge as it is technical. Current political economy contexts – whether national, regional or global – condition the ways STI systems in SSA evolve, the goals they prioritise, and which STI system actors secure economic benefits and power. We summarise a political economy analysis of the STI systems in five SSA countries – Ethiopia, Kenya, Rwanda, Senegal and Tanzania – and provide recommendations relevant to each national case, especially for each national Science Granting Council (SGC). We also highlight common themes that emerge from the cases and give recommendations for action across SSA more generally. Important cross-cutting issues are that gender and inclusivity do not seem to be receiving the active attention they need if they are to be addressed sufficiently in line with sustainability goals, and human resource constraints continue to hamper efforts to strengthen STI systems.