Human perceptions and concerns about the implications of climate change have a profound importance for adaptation to and mitigation of the impacts of climate change at various scales and in different economic and social sectors in a given geographical landscape. Although studies on public perceptions of climate change are increasing globally, they are still scant pertaining to the Himalayan region of Nepal. In order to fill this gap, this study aimed to understand individual and community perceptions of climate change in the Lower Mustang region of Nepal, where apple farming and agricultural activities have been significantly impacted by climate change over the last 30–40 years. The data collection for the study included a cross-sectional survey of 200 farmers with a structured questionnaire, seven focus group discussions, and 26 key informant interviews, which were administered in four rural municipalities: Kagbeni, Jomsom, Marpha, and Tukuche. Results of the study indicated that a majority of the participants experienced an increase in temperature with warmer summers (99% of the participants surveyed), a decrease in snowfall (100%), and variable rainfall patterns (87%). However, the warming climate-enhanced diversification of vegetables in Lower Mustang, and the changes in climatic patterns over the years have affected almost all the agricultural systems of the region. In particular, apple farming in lower elevations has been negatively impacted due to decreasing snowfall, necessitating an urgent attention to develop sustainable adaptation strategies in order to minimize the deleterious impacts of the changing climatic patterns.