Abstract Background To explore the impacts of contextual issues encompassing social, cultural, political and institutional elements, on the operation of public health surveillance systems in Nepal concerning the monitoring of infectious diseases in the face of a changing climate. Methods Semi-structured interviews (n = 16) were conducted amongst key informants from the Department of Health Services, Health Information Management System, Department of Hydrology and Meteorology, World Health Organization, and experts working on infectious disease and climate change in Nepal, and data were analysed using thematic analysis technique. Results Analysis explicates how climate change is constructed as a contingent risk for infectious diseases transmission and public health systems, and treated less seriously than other ‘salient’ public health risks, having implications for how resources are allocated. Further, analysis suggests a weak alliance among different stakeholders, particularly policy makers and evidence generators, resulting in the continuation of traditional practices of infectious diseases surveillance without consideration of the impacts of climate change. Conclusions We argue that along with strengthening systemic issues (epidemiological capacity, data quality and inter-sectoral collaboration), it is necessary to build a stronger political commitment to urgently address the influence of climate change as a present and exponential risk factor in the spread of infectious disease in Nepal.