Abstract Monitoring the extent and pattern of snow cover in the dry, high altitude, Trans Himalayan region (THR) is significant to understand the local and regional impact of ongoing climate change and variability. The freely available Moderate Resolution Imaging Spectroradiometer (MODIS) snow cover images, with 500 m spatial and daily temporal resolution, can provide a basis for regional snow cover mapping, monitoring and hydrological modelling. However, high cloud obscuration remains the main limitation. In this study, we propose a five successive step approach — combining data from the Terra and Aqua satellites; adjacent temporal deduction; spatial filtering based on orthogonal neighbouring pixels; spatial filtering based on a zonal snowline approach; and temporal filtering based on zonal snow cycle — to remove cloud obscuration from MODIS daily snow products. This study also examines the spatial and temporal variability of snow cover in the THR of Nepal in the last decade. Since no ground stations measuring snow data are available in the region, the performance of the proposed methodology is evaluated by comparing the original MODIS snow cover data with least cloud cover against cloud-generated MODIS snow cover data, filled by clouds of another densely cloud-covered product. The analysis indicates that the proposed five-step method is efficient in cloud reduction (with average accuracy of > 91%). The results show very high interannual and intra-seasonal variability of average snow cover, maximum snow extent and snow cover duration over the last decade. The peak snow period has been delayed by about 6.7 days per year and the main agropastoral production areas of the region were found to experience a significant decline in snow cover duration during the last decade.