Following 50 years of apartheid, South Africa introduced visionary health policy committing to the right to health as part of a primary health care (PHC) approach. Implementation is seriously challenged, however, in an often-dysfunctional health system with scarce resources and a complex burden of avoidable mortality persists. Our aim was to develop a process generating evidence of practical relevance on implementation processes among people excluded from access to health systems. Informed by health policy and systems research, we developed a collaborative learning platform in which we worked as co-researchers with health authorities in a rural province. This article reports on the process and insights brought by health systems stakeholders. Evidence gaps on under-five mortality were identified with a provincial Directorate after which we collected quantitative and qualitative data. We applied verbal autopsy to quantify levels, causes and circumstances of deaths and participatory action research to gain community perspectives on the problem and priorities for action. We then re-convened health systems stakeholders to analyse and interpret these data through which several systems issues were identified as contributory to under-five deaths: staff availability and performance; service organization and infrastructure; multiple parallel initiatives; and capacity to address social determinants. Recommendations were developed ranging from immediate low- and no-cost re-organization of services to those where responses from higher levels of the system or outside were required. The process was viewed as acceptable and relevant for an overburdened system operating 'in the dark' in the absence of local data. Institutional infrastructure for evidence-based decision-making does not exist in many health systems. We developed a process connecting research evidence on rural health priorities with the means for action and enabled new partnerships between communities, authorities and researchers. Further development is planned to understand potential in deliberative processes for rural PHC.