IntroductionHealth policy and systems research (HPSR) is a multi-disciplinary approach of generating health system and policy-level evidence. Setting HPSR agendas is considered as an efficient strategy to map and identify policy and cost-effective research topics, but its practice in developing countries is limited. This paper aimed to conduct a collaborative health policy and system research priority-setting exercise in Ethiopia.MethodThe WHO’s plan, implement, publish, and evaluate (PIPE) framework and the Delphi technique were used to conduct the priority-setting exercise. The PIPE model was used to lead the priority-setting process from planning to evaluation, while the Delphi technique was used to run the rating and ranking exercise with the aim of reaching a consensus. Two rounds of expert panel workshops supplemented with an online survey were used for the HPSR agenda setting, rating and ranking purposes. Groups were formed using the WHO health system building blocks as a base framework to identify and prioritize the HPSR topics.ResultUnder 8 themes, 32 sub-themes and 182 HPSR topics were identified. The identified research themes include leadership management and governance, health policy, health information system, healthcare financing, human resource for health, medical products and supply, service delivery and cross-cutting issues.ConclusionsPriority HPSR topics focussing on national health priority issues were identified. The identified topics were shared with policymakers and academic and research institutions. Evidence generation on the identified priority topics will guide future research endeavours and improve evidence-informed decision-making practice, health system performance and national health goals and targets.