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Health information systems (HIS) are used to manage information related to population health. The goal of this research was to conduct an evaluation of a HIS used at a hospital in south-western Uganda using participatory approaches. The evaluation structure was based on guidelines generated by the Center for Disease Control and Prevention and a series of theoretical and methodological concepts regarding participatory engagement that encouraged stakeholder participation throughout the evaluation. The primary objectives were to describe the areas of strength and limitations of the HIS, and develop potential system enhancements. Ultimately, engagement of local staff members throughout each stage of the evaluation resulted in the development of a series of recommendations considered relevant and feasible by local stakeholders. We build on these results by highlighting the value of stakeholder engagement and opportunities to apply participatory and community-based research methods and an Ecohealth framework to an HIS evaluation.