Despite increasing attention to geologically recent extinctions in the ocean, little information is available on natural distributions of extinct species before contact with humans. In the North Pacific, a large cormorant, Phalacrocorax perspicillatus (Spectacled/Pallas's Cormorant), was driven to extinction in the 19th century, probably due to overexploitation by humans. So far, no clear evidence has existed for the past presence of the cormorant species outside Bering Island, Commander Islands. We report fossil remains of P. perspicillatus from the upper Pleistocene (Marine Isotope Stage 5e, ∼120,000 yr ago) of Shiriya, northeast Japan. The occurrence is the first definitive record of the species outside Bering Island, and the first pre-Holocene record for the species, expanding the known geographic and temporal ranges of the species by ∼2,400 km and ∼120,000 yr, respectively. It indicates that the species had undergone a drastic range contraction or shift since the Pleistocene, probably before the first contact with humans. Available evidence indicates a drop of oceanic productivity near Shiriya in the Last Glacial Maximum (∼17,000 yr ago), which might have affected the local population of the cormorant species and possibly led to the species' local disappearance from this area. In any case, the population of P. perspicillatus on Bering Island at its first scientific discovery should be considered a relict.