Several large and rapid changes in atmospheric temperature and the partial pressure of carbon dioxide in the atmosphere1—probably linked to changes in deep ocean circulation2—occurred during the last deglaciation. The abrupt temperature rise in the Northern Hemisphere and the restart of the Atlantic meridional overturning circulation at the start of the Bølling–Allerød interstadial, 14,700 years ago, are among the most dramatic deglacial events3, but their underlying physical causes are not known. Here we show that the release of heat from warm waters in the deep North Atlantic Ocean probably triggered the Bølling–Allerød warming and reinvigoration of the Atlantic meridional overturning circulation. Our results are based on coupled radiocarbon and uranium-series dates, along with clumped isotope temperature estimates, from water column profiles of fossil deep-sea corals in a limited area of the western North Atlantic. We find that during Heinrich stadial 1 (the cool period immediately before the Bølling–Allerød interstadial), the deep ocean was about three degrees Celsius warmer than shallower waters above. This reversal of the ocean's usual thermal stratification pre-dates the Bølling–Allerød warming and must have been associated with increased salinity at depth to preserve the static stability of the water column. The depleted radiocarbon content of the warm and salty water mass implies a long-term disconnect from rapid surface exchanges, and, although uncertainties remain, is most consistent with a Southern Ocean source. The Heinrich stadial 1 ocean profile is distinct from the modern water column, that for the Last Glacial Maximum and that for the Younger Dryas, suggesting that the patterns we observe are a unique feature of the deglacial climate system. Our observations indicate that the deep ocean influenced dramatic Northern Hemisphere warming by storing heat at depth that preconditioned the system for a subsequent abrupt overturning event during the Bølling–Allerød interstadial.