We studied the functional morphology of the postcranial skeleton of the endemic hippopotamus Phanourios minor, derived from the Upper Pleistocene site of Ayia Napa. The deposit, which consists of a hard limestone substrate on which the species moved, has yielded a great abundance of hippopotamus material, making the Ayia Napa locality one of the most important paleontological sites in Cyprus. The immigration of the large‐sized mainland Hippopotamus to Cyprus led to the emergence of a new insular species with its main characteristic being the extremely reduced body size. In this study, all the hindlimb elements of the Cypriot hippo are described in detail and compared with those of the modern species, with the extant Hippopotamus amphibius being considered similar to the possible ancestor of P. minor. In some cases, the morphological comparison is reinforced using bones of other extinct insular and mainland hippos. Additionally, we provided a functional analysis of the hindlimb joints, suggesting specific locomotor habits for the species. The anatomical examination reveals that the elements in P. minor are robust with marked muscular insertion areas resembling those found in Hippopotamus. However, there are also similarities with Choeropsis liberiensis in certain morphofunctional traits. P. minor adapted to slow but powerful locomotion with remarkable stabilization, particularly in the zeugopodium and the autopodium. The knee was less mobile in the craniocaudal direction compared with that in recent hippos, while the abduction–adduction movements of the thigh were advanced. The pes presented good mobility in the sagittal plane and limitation in transversal movements. Thus, P. minor displayed modifications to its limbs, influenced by the mountainous island environment and the body size reduction, resulting in specialized locomotion, which was different from that of extant hippopotamuses.