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Background: Frontline managers and health service providers are constrained in many contexts from responding to community priorities due to organizational cultures focused on centrally defined outputs and targets. This paper presents an evaluation of the Verbal Autopsy with Participatory Action Research (VAPAR) programme—a collaborative learning platform embedded in the local health system in Mpumalanga, South Africa—for strengthening of rural primary healthcare (PHC) systems. The programme aims to address exclusion from access to health services by generating and acting on research evidence of practical, local relevance. Methods: Drawing on existing links in the provincial and national health systems and applying rapid, participatory evaluation techniques, we evaluated the first action-learning cycle of the VAPAR programme (2017–19). We collected data in three phases: (1) 10 individual interviews with programme stakeholders, including from government departments and parastatals, nongovernmental organizations and local communities; (2) an evaluative/exploratory workshop with provincial and district Department of Health managers; and (3) feedback and discussion of findings during an interactive workshop with national child health experts. Results: Individual programme stakeholders described early outcomes relating to effective research and stakeholder engagement, and organization and delivery of services, with potential further contributions to the establishment of an evidence base for local policy and planning, and improved health outcomes. These outcomes were verified with provincial managers. Provincial and national stakeholders identified the potential for VAPAR to support engagement between communities and health authorities for collective planning and implementation of services. Provincial stakeholders proposed that this could be achieved through a two-way integration, with VAPAR stakeholders participating in routine health planning and review activities and frontline health officials being involved in the VAPAR process. Findings were collated into a revised theory of change. Conclusions: The VAPAR learning platform was regarded as a feasible, acceptable and relevant approach to facilitate cooperative learning and community participation in health systems. The evaluation provides support for a collaborative learning platform within routine health system processes and contributes to the limited evaluative evidence base on embedded health systems research.