BackgroundThe Nepalese Government has made significant progress toward the elimination of malaria. However, given the surge in the prevalence of non-communicable diseases, such as diabetes and hypertension, and the localized nature of malaria prevalence, malaria elimination will remain a challenge. In the current study, the authors sought to understand local perceptions on threats to malaria elimination in three endemic districts.MethodsThe authors conducted a capacity-building exercise embedded within a qualitative study. The study component aimed to understand how local policymakers and actors perceive challenges in malaria elimination. For them to be able to articulate the challenges, however, an understanding of malaria elimination in the context of a broader health system in Nepal would be required. The capacity-building component, thus, involved providing that knowledge.ResultsAlthough the prevalence of malaria is high in the three districts where the study was conducted, there are significant gaps in human resources, diagnosis and treatment, and the provision of indoor residual spraying and long-lasting insecticide treated nets. More importantly, the authors’ experience suggests that it may be possible to capitalize on local expertise in order to identify gaps in malaria elimination at a sub-national level by building in a capacity-building exercise within a study.ConclusionsLocals in three malaria-endemic districts of Nepal perceive that there are significant gaps in human resources, diagnosis and treatment, the provision of insecticide treated nets, and indoor residual spraying.