We report here on the process and findings of a research prioritisation exercise for universal health coverage (UHC) in South Africa, conducted during the course of 2019. As plans to roll out National Health Insurance (NHI) gather momentum and we transition into a pandemic recovery phase, we believe that it is now time to revisit these priorities, while recognising that experiences with the COVID-19 pandemic have revealed new system challenges and strengths and introduced new priorities. The UHC research priority-setting methodology followed a stepwise process of collation of evidence, expert brainstorming and the development of a survey completed by 68 members of the Public Health Association of South Africa. Themes related to leadership and governance were ranked most highly, and with other priorities generated, provide an initial road map of knowledge needs that could guide individual institutions and commissioning by funding bodies. We further reflect on the importance of researcher-decision-maker dialogue and strengthening the contribution of health policy and systems research to policy and practice, especially as new reforms are implemented.