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Background: Health research governance is an essential function of national health research systems. Yet many African countries have not developed strong health research governance structures and processes. This paper presents a comparative analysis of national health research governance in Botswana, Kenya, Uganda and Zambia, where health sciences research production is well established relative to some others in the region and continues to grow. The paper aims to examine progress made and challenges faced in strengthening health research governance in these countries., Methods: We collected data through document review and key informant interviews with a total of 80 participants including decision-makers, researchers and funders across stakeholder institutions in the four countries. Data on health research governance were thematically coded for policies, legislation, regulation and institutions and analysed comparatively across the four national health research systems., Results: All countries were found to be moving from using a research governance framework set by national science, technology and innovation policies to one that is more anchored in health research structures and policies within the health sectors. Kenya and Zambia have adopted health research legislation and policies, while Botswana and Uganda are in the process of developing the same. National-level health research coordination and regulation is hampered by inadequate financial and human resource capacities, which present challenges for building strong health research governance institutions., Conclusion: Building health research governance as a key pillar of national health research systems involves developing stronger governance institutions, strengthening health research legislation, increasing financing for governance processes and improving human resource capacity in health research governance and management., (© 2021. The Author(s).)