Urbanisation has threatened native forests globally with remaining forests often existing as small isolated patches in a harsh landscape matrix. Devoid of large predators, forest patches may continue to support ungulate populations, but their conservation is challenging as unchecked population growth can bring about ecosystem imbalances and threaten other native species. Three ungulate species exist in small rainforest fragments of urbanised Singapore: the locally endangered lesser mouse-deer (Tragulus kanchil), and the re-emergent wild boar (Sus scrofa) and sambar deer (Rusa unicolor). Using an array of camera traps, we estimated the densities of the lesser mouse-deer, wild boar and sambar deer in rainforest patches, and determined the influence of habitat and landscape factors on their occupancies. We also studied the interactions of the wild boar and sambar deer with the lesser mouse-deer spatially and temporally. Estimates of the lesser mouse-deer density showed that the population has recovered since the 1990s. Its density was comparable to the wild boar, but higher than sambar deer. Detections of lesser mouse-deer were significantly higher in primary forests compared to old secondary forests, and increasing distance away from the nearest road or public trail was a strong predictor of its occupancy. There was no evidence that the wild boar and sambar deer competitively excluded the lesser mouse-deer, rather, co-occupancy was observed. We demonstrated that temporal niche partitioning between the lesser mouse-deer and the two other ungulates likely explained their co-existence. Notwithstanding this, there are indications of understorey alteration due to the wild boar occurrences. Thus, continued monitoring of ungulate populations and conservation efforts focused on maintaining the health of the primary and secondary rainforest patches, and reducing disturbance, are critical to sustain future populations of lesser mouse-deer. Our study has shed new light on the habitat use and species interactions of tropical ungulates in urban predator-free ecosystems and highlight the importance in gaining a deeper understanding of their dynamics to more effectively guide conservation and management decisions.