Apex predators live at the top of an ecological pyramid, preying on animals in the pyramid below and normally immune from predation themselves. Apex predators are often, but not always, the largest animals of their kind. The living killer whale Orcinus orca is an apex predator in modern world oceans. Here we focus on an earlier apex predator, the late Eocene archaeocete Basilosaurus isis from Wadi Al Hitan in Egypt, and show from stomach contents that it fed on smaller whales (juvenile Dorudon atrox) and large fishes (Pycnodus mokattamensis). Our observations, the first direct evidence of diet in Basilosaurus isis, confirm a predator-prey relationship of the two most frequently found fossil whales in Wadi Al-Hitan, B. isis and D. atrox. This extends our understanding of their paleoecology. Late Eocene Basilosaurus isis, late Miocene Livyatan melvillei, and modern Orcinus orca are three marine apex predators known from relatively short intervals of time. Little is known about whales as apex predators through much of the Cenozoic era, and whales as apex predators deserve more attention than they have received.