We performed postmortem examinations on seven Misaki feral horses (Equus caballus) and evaluated Misaki feral horses, Japanese wild boars (Sus scrofa leucomystax), domestic pigs (Sus scrofa), and wild Japanese macaques (Macaca fuscata fuscata) from 2015 to 2017 in Cape Toi, Kushima, Miyazaki Prefecture, southern Japan, for antibodies against Japanese encephalitis virus (JEV). Strongylus vulgaris infection with severe arterial lesions and hemomelasma ilei was present in all necropsied horses. We frequently found intestinal ulcers, perihepatitis filamentosa, and poor body condition. We recorded degenerative arthropathy in metacarpophalangeal joints in two cases and a fracture of the rib with diaphragmatic rupture in one case. A total of 73% (177/242) of horses were seropositive for JEV as tested by hemagglutination inhibition (HI). The HI data also revealed that 74% (59/80) of the wild boars, 67% (60/90) of the pigs, and 29% (22/75) of the wild monkeys were seropositive for JEV. Our findings showed that Strongylus spp. are still a risk to horses in this region, and that environmental factors such as topographic location of the pasture and steep slope may have caused of degenerative arthropathy and bone fracture. Our results showed that JEV is endemic in Japan. The wild boars and pigs were presumed to act as strong amplifiers and sources of infection, with subsequent risk to humans.