Limnonectes paginatanensis is a lowland species endemic to Sabah. In certain areas, Limnonectes paginatanensis may occur with other related species. It has been reported sympatric with L. tawauensis at Poring (Kinabalu), Sabah. According to Matsui et al. (2024) the two species can be distinguished by differences in digital disks (wider disk of third and fourth finger in L. paginatanensis) and tibial warts (much less warts in L.p.). 

This species measures on average 55 mm snout to vent in males and 56 mm in females, so sexual dimorphism is not pronounced. 

According to Matsui et al. (2024) the new species can be distinguished from its close relatives by the combination of: The dorsal skin, which is extremely folded and features networks of wrinkles running in all directions, scattered with warts posterior to the sacrum. The tibia is dorsally coarsely scattered with small warts with white tips. The first finger is slightly longer than the second, and the tip of the third finger forms a large disk that is slightly wider than the basal phalanges. The tip of the fourth toe is swollen into a large disk that is much wider than the basal phalanx, and the fourth toe is broadly webbed to the disk. The head is relatively short (in comparison to other close relatives), the forelimb and hindlimb are medium, and the tibia is short. The outer edges of the second and third fingers have moveable dermal flaps. The fourth toe disk is much wider than the third finger disk, and the inner and outer webbing of the fourth toe is slightly excised. The dorsum is dark brown without markings, the throat and chest are brown reticulated with cream.