The main objective of this study was to identify and prioritize subbasins/watersheds in the Middle and High Mountains of Nepal that are significantly vulnerable to Climate Change (CC). The approach of the vulnerability assessment framework of the United Nation’s Intergovernmental Panel on Climate Change (IPCC) was the guide for this study. The data integration and aggregation approach, by constructing indices, was adopted to integrate different types of indicators representing the dimensions of sensitivity, exposure and adaptive capabilities of climate change and vulnerability. The National Adaptation Program of Action (NAPA) is a strategic tool and framework used to respond to climate change adaptation issues in Nepal and was mandated to assess the climatic variability and impacts throughout the country. This study has used the NAPA assessment as a starting point but has added several biophysical and socioeconomic criteria, which were seen as relevant at the watershed level. Therefore, although it has been built upon the NAPA assessment, it is more comprehensive and at a higher spatial resolution, which is geared towards management interventions at the watershed level.