The grey whale (Eschrichtius robustus), once present in both the eastern and western North Atlantic, is the only whale species to have been extirpated from an ocean in historical times. For several centuries the species has been confined to the North Pacific, with the exception of isolated vagrants in recent decades that may be harbingers of its return to the Atlantic. Yet the chronology and causation of the past Atlantic extirpation have been unclear. A new radiocarbon dating programme applied as part of this study, including archaeological and palaeontological grey whale specimens from mainly European contexts, reveals the past spatiotemporal range of the species in the eastern North Atlantic as inferred from subfossil evidence. The new radiocarbon evidence dates the extirpation to between the mid twelfth and mid fourteenth centuries CE, earlier than previously assumed and a period of pre-industrial, yet extensive, European whaling activity undertaken by several medieval societies along the likely migration route of this coastal species. Pre-modern whaling may thus have contributed to this first anthropogenically driven extirpation of a whale species from an ocean and, by extension, eliminated the grey whale’s distinctive and important ecosystem services, such as sediment reworking and near-coastal translocation of nutrients, from the eastern North Atlantic.