During 1997–2012 we conducted a nationwide camera-trapping survey and assessed the availability of prey and habitat for the clouded leopard Neofelis nebulosa in Taiwan. We surveyed 1,249 camera-trap sites over 113,636 camera-trap days, from the seashore to an altitude of 3,796 m and covering various types of vegetation. No clouded leopards were photographed during 128,394 camera-trap days, including at 209 sites in other studies, confirming the presumed extinction of clouded leopards in Taiwan. Assessment of the prey base revealed altitudinal distribution patterns of prey species and prey biomass. Areas at lower altitudes and with less human encroachment and hunting supported a higher prey biomass and more of the typical prey species of clouded leopards. Habitat analysis revealed 8,523 km2 of suitable habitat but this was reduced to 6,734 km2 when adjacent areas of human encroachment were subtracted. In the absence of hunting and large mammalian carnivores the major prey of clouded leopards in Taiwan, such as Formosan macaques Macaca cyclopis, Reeves's muntjacs Muntiacus reevesi, Formosan serow Capricornis swinhoei and sambar Rusa unicolor, could become over-abundant. Thus, it is important to address the cascading effect of the disappearance of top-down predator control. Our assessment indicated that, with proper regulation of hunting, habitat restoration and corridor improvement, it may be possible to reintroduce the clouded leopard.