The Japanese archipelago has long been perceived as an insular environment with a naturally impoverished predator assemblage. However, historical and biogeographical evidence suggests that Japan once supported a diverse array of large predators, including tigers (Panthera tigris acutidens), leopards (Panthera pardus), and wolves (Canis lupus hodophilax), alongside aquatic and avian predators such as the Japanese otter (Lutra nippon) and golden eagle (Aquila chrysaetos). This review reconstructs Japan’s late Quaternary predator communities and their extirpation, synthesizing paleoecological, archaeological, and historical data. Land bridges connecting Hondo—the combined landmass of Honshu, Kyushu, and Shikoku—to the Korean Peninsula and Taiwan facilitated predator colonization during glacial periods, fostering an ecosystem similar to mainland Asia. However, the arrival of human populations, particularly the Jomon people, triggered cascading extinctions. Overhunting of megafaunal prey, such as Sinomegaceros yabei, led to the collapse of apex predator populations, while habitat changes, including coniferous forest expansion due to the absence of megafauna grazing, further altered ecosystem dynamics. The disappearance of Japan’s large predators caused unchecked herbivore proliferation, mesopredator release, carrion food web disruption, and reduced nutrient cycling efficiency. Modern conservation challenges, such as golden eagle and giant salamander declines, mirror historical extinction patterns, highlighting the continued effects of habitat change in predator loss. We argue that defining an appropriate biodiversity baseline is essential for conservation efforts in Japan, challenging the paradigm that insularity naturally limits predator diversity. The widespread extinctions of Japan’s apex predators resulted from human actions, not geographical constraints, and modern conservation policies must acknowledge this history. By integrating historical ecology into conservation, Japan can move toward a more ecologically informed management approach, including potential rewilding initiatives. Recognizing the unnatural history of Japan’s predators is crucial for restoring lost ecosystem functions and mitigating the cascading effects of past extinctions.