Background: The 58th world health assembly in 2004 and the 2008 Bamaka call to action emphasized the use of evidence as an essential priority to achieve health equity. The attainment of high-quality research begins with a strong national health research system that generates, disseminates, and uses evidence. Research agendas have been shown to maximize the efficiency and effectiveness of research investments, strengthen health research systems, and harmonize research priorities across stakeholders. Despite recognition of research agendas as an important tool for health improvement and resource optimization, most of these do not include an evaluation plan. First published in 2006, the Philippine national unified health research agenda (NUHRA) is intended to guide national health research activity, generate research support, and promote the translation of research into practice. The NUHRA 2017-2022 was informed by international, national, and regional research priorities. This evaluation aimed to provide data for its implementers for decision-making, implementation improvement, and subsequent research agenda formulation. Methods: The evaluation applied a mixed method approach with a triangulation convergence model. An evaluation plan was developed based on a literature review of global research agenda evaluation literature and policy review of NUHRA implementation. Secondary quantitative data collection focused on research output metrics from all regions of the Philippines. Primary data was collected through 40 key informant interviews of national and regional health research council members, NUHRA implementers, and researchers. Data will be analyzed through descriptive and thematic analysis using an abductive approach. Results and Discussion: This project evaluated the NUHRA 2017-2022 using secondary data from regions and interviews with research stakeholders across regions and members/nonmembers of research consortiums. The findings emphasize the importance of mobilizing resources for research, a robust monitoring system to maintain relevance of research priorities, and improving the relationship between researchers and policymakers to facilitate evidence-based decision making.