Background: Currently the health research system in Lao PDR is fragmented and largely donor led. Capacity among national public health institutes is limited to select priority research questions for funding. Objective: The objective of this capacity building and practice-oriented study is to describe the process and outcome of the first National Health Research Agenda for Lao PDR and how the agenda contributes to institutional capacity of the Ministry of Health, in order to contribute to evidence-informed public health policy making. Method: This activity used a mixed-methods approach. The overall design is based on principles of the interactive Learning and Action approach and consists out of 6 phases: (1) identification of needs, (2) shared analysis and integration, (3) nationwide prioritization of research domains, (4) exploring specific research questions, (5) prioritization of research avenues, (6) dialogue and planning for action. The process involved interviews with experts in health policy and research (n = 42), telephone-based survey with district, provincial and national health staff (n = 135), a two-round Delphi consultation with experts in health policy and research (n = 33), and a workshop with policymakers, researchers, international organisations and civil society (n = 45) were held to gather data and conduct shared analysis. Results: 11 research domains were identified and prioritised: Health-seeking behaviour; Health system research; Health service provision; Mother and child health (MCH); Sexual & reproductive health; Health education; Non-communicable diseases (NCDs); Irrational drug use; Communicable diseases (CDs); Road traffic accidents; Mental health. Within these domains over 200 unique research questions were identified. Conclusion: Our approach led to a comprehensive, inclusive, public health agenda for Lao PDR to realise better informed health policies. Questions on the agenda are action-oriented, originating in a desire to understand the problem so that immediate improvements can be made. The agenda is used within the MoH as a tool to fund and approve research.