Asian elephants are isolated in fragmented habitat patches in and around Bardia National Park (BNP), Nepal. To describe habitat use patterns and ecogeographical variables (EGVs) that determine an elephant’s niche in BNP, we used a General Niche-Environment System Factor Analysis (GNESFA) modeling framework. Novel to our study was the comparison of niche requirements between core (residential) and corridor (travel corridor) areas to elucidate site-specific preferences of Asian elephants in BNP. A total of 13 EGVs (four topographic variables, six land covers, heterogeneity index and two anthropogenic variables) were examined. We implemented a ‘bias file’ approach to address potential sampling bias in the transect survey methods for presence records. Our study illustrated that, regardless of study area, elephants’ habitat use was positively influenced by presence of grasslands, mixed forest, and landscape heterogeneity, whereas use was restricted by the topographic variables of slope and elevation. Results also demonstrated different habitat preferences between elephants in the core and corridor, which may be attributed to differences in potential dangers posed in these areas; in the core, elephant habitat preference was mainly associated with food resources such as grassland or mixed forest, whereas in the corridor, where elephants are more likely to encounter human conflict, the anthropogenic factor of distance to human settlements contributed the most in predicting elephant presence. Correlations among significant factors from the three methods (FANTER, ENFA, and MADIFA) demonstrated the consistent and reliable results of these approaches. While these methods complemented each other by providing different points of view, FANTER was especially useful when bimodal niches were analyzed. We suggest a detailed conservation plan for the small populations of elephants in BNP and surrounding areas, while considering the protection of travel routes from human activities in the corridor habitats, and lastly, maintaining grasslands and waterholes in core habitats.