Wild ungulate herbivores are crucial for maintaining terrestrial ecosystems and restoring population of top predators like tiger. Thus, it is essential to understand wild ungulates-habitat relationships to devise an effective strategy to conserve their population and top predators like tiger that depend on them. We have limited understanding about the ungulates and their habitat in sub-tropical lowlands. In this study, we conducted transect based occupancy surveys in December 2016 across 30 geographic grid cells of 3 km × 3 km spanning 270 km2. We used the occupancy modelling approach that accounts for the imperfect detection to test multiple hypotheses concerning ecological and anthropogenic correlates of site use pattern of five wild ungulate species in Shuklaphanta National Park, Nepal. The model-average estimates showed that proportion of site use was highest for spotted deer (0.83 ± SE 0.29) followed by blue bull (0.53 ± SE 0.22), hog deer (0.37 ± SE 0.12), swamp deer (0.23 ± SE 0.17), and lowest for barking deer (0.14 ± SE 0.05). While the proportion of forest had a positive influence on blue bull and barking deer, the proportion of grassland had a positive influence on spotted deer and swamp deer. Water availability positively influenced site use of barking deer. Human disturbance had a strong negative influence on the distribution of hog deer but blue bull had a positive association with human activities. Similarly, fire had a strong positive influence only on the habitat use of swamp deer. Overall, our results showed that these five wild ungulate species vary in their site use responses to natural habitat and anthropogenic factors suggesting that the consideration of species-specific habitat requirements is important for their conservation and management.