High species diversity and endemism within a vast area of intact and unexplored landscapes makes the eastern Himalayas a global biodiversity hotspot. It houses 75 globally threatened mammal species including the iconic tiger Panthera tigris and snow leopard Uncia uncia. We mapped priority areas for 255 native terrestrial mammal species in the Eastern Himalayas using current IUCN Red List spatial data, and identified centres of species richness at a spatial scale of 1×1 km using a GIS framework and the R-package ‘LetsR’. To assess the degree of protection to priority areas, we calculated the percentage of a threatened species’ range that fell within protected areas, and developed a comparison index to conduct gap analysis and representativeness of geophysical features (physiography, altitude, and eco-regions). Although the extent of protected areas in the eastern Himalayas has increased significantly over the last four decades, the regions’ threatened mammal species are still under represented in protected areas and facing substantial anthropogenic threats from habitat loss and illegal hunting. Our results indicate skewedness in the pattern of mammal diversity, afforded level of protection, and distribution of protected areas among range countries. Despite this, Bhutan‘s network of protected areas and biological corridors is effective in conserving several threatened Eastern Himalayan mammal species at a finer scale. As the Eastern Himalayan landscape is shared by five countries, regional cooperation for effective transboundary research and management through collaborative efforts is necessary, and regional prioritisation of areas for biodiversity conservation is essential for preventing species extinctions.