The Indian pangolin (Manis crassicaudata), the only member of order “Pholidota” occurring in Pakistan, is threatened by the rampant trade of the species, and has been listed as “Endangered” since 2014. The current study investigated the occupancy, habitat suitability and habitat preference of pangolin in the Potohar Plateau and Azad Jammu & Kashmir. A Single-season model was used to analyze the data in PRESENCE software to document occupancy of species. The presence/absence data for 240 grids with 10 sampling occasions (2400 survey plots) and 45 missing observations analyzed this model. The data collected from sampling plots along with environmental layers (including; elevation, slope, land cover, distance to nearest settlement) and bioclimatic layers (including annual mean temperature and precipitation) were processed to generate habitat suitability maps in MaxEnt software. To document habitat preference, we stratified the habitat of Indian pangolin into three different habitat types; forests, agricultural lands and grasslands. Estimated naïve occupancy was 0.3167 whereas detection probability was estimated as 0.32 ± 0.03(SE), which suggests 32% of the study area is occupied by the Indian Pangolin. The MaxEnt analysis showed that out of 26872.52 km² area available to Indian pangolin, 1674 km² (6.2%) was highly suitable habitat, followed by 3851.7 km² (14.3%) suitable habitat, 8438.3 km² (31.4%) less suitable habitat and 12908.2 km² (48%) not suitable habitat, although lack of signs does not necessarily equate to lack of habitat suitability and hunting pressure and other factors, independent of habitat suitability, can strongly influence occupancy. The Jackknife test of variable contribution, revealed that elevation was the most important predictor variable as measured by the gain produced by a one-variable model, followed by, average temperature, settlement, land class, slope and aspect. Among three different types of habitats studied, forest was found to be more preferred, followed by agricultural land habitat whereas grassland was used least by the species.