The Indian pangolin (Manis crassicaudata), an elusive and endangered species, remains understudied in Pakistan. This study presents a detailed ecological baseline of the spatial distribution, population density, burrow typology, vegetation associations, and threats to the species in District Buner, Khyber Pakhtunkhwa, from October 2022 to September 2023. Using stratified random sampling across 90 km², surveys along line transects and circular plots identified 127 burrows across four tehsils, with 63.8% of the burrows being active, 26.0% inactive, and 10.2% living/resting burrows. The most active burrows occurred between 300 and 700 m elevation, with a few found up to 1,300 m, and were absent above this range. Burrow activity was highest in Mandanr Tehsil, with a preference for north- and east-facing slopes, loamy soils, rocky substrates, moderate canopy cover (41–70%), and dense understory. Distance sampling estimated a low population density of 0.43 individuals/km², indicating a sparse and uneven distribution. The Phyto habitat associations linked living burrows to Lantana camara and Punica granatum, whereas feeding sites correlated with Dalbergia sissoo, Acacia modesta, and prey-rich substrates. Burrow concentration was highest in ecotones between scrub and subtropical pine forests, whereas areas dominated by Pinus roxburghii, Juglans regia, and Quercus incana lacked any signs of presence. Two direct sightings and physical remains confirmed the presence and local extirpation at some sites. The primary threats include poaching, illegal trade, habitat degradation, marble mining and unregulated development. These issues are exacerbated by weak law enforcement and low local awareness. This study provides the first fine-scale ecological baseline for M. crassicaudata in the Western Himalayas. Conservation recommendations include habitat restoration, zoning, anti-poaching enforcement and community-based monitoring. These findings serve as a foundation for developing integrated conservation strategies tailored to the region’s unique ecological and sociopolitical contexts.