Earthquake hazard assessments for the Tokyo Region are complicated by the trench–trench triple junction where the oceanic Philippine Sea Plate not only underthrusts a continental plate but is also being subducted by the Pacific Plate. Great thrust earthquakes and associated tsunamis are historically recognized hazards from the Continental/Philippine Sea (Sagami Trough) and Continental/Pacific (Japan Trench) plate boundaries but not from the Philippine Sea/Pacific (Izu–Bonin Trench) boundary alone. Here we employed a series of historical and hypothetical rupture models to explain the widespread distribution of geological evidence for an unusually large tsunami found along 50 km of coastline east of Tokyo. Dating to about 1,000 years ago, this inferred tsunami predates local written history by several hundred years. We found that the inland extent of its sand sheet is best explained, in computer simulations, by displacement on one of the three plate boundaries offshore of the Boso Peninsula, which corresponds to the triple junction. The minimum magnitude scenario capable of generating the inland extent of inundation involves displacement along the Philippine Sea/Pacific boundary megathrust. This plate-boundary fault adds another potential source for earthquakes in the Tokyo Region and tsunamis in the Pacific Ocean.