The Greenland Ice Sheet (GIS) contains the equivalent of 7.4 metres of global sea-level rise. Its stability in our warming climate is therefore a pressing concern. However, the sparse proxy evidence of the palaeo-stability of the GIS means that its history is controversial (compare refs 2 and 3 to ref. 4). Here we show that Greenland was deglaciated for extended periods during the Pleistocene epoch (from 2.6 million years ago to 11,700 years ago), based on new measurements of cosmic-ray-produced beryllium and aluminium isotopes (10Be and 26Al) in a bedrock core from beneath an ice core near the GIS summit. Models indicate that when this bedrock site is ice-free, any remaining ice is concentrated in the eastern Greenland highlands and the GIS is reduced to less than ten per cent of its current volume. Our results narrow the spectrum of possible GIS histories: the longest period of stability of the present ice sheet that is consistent with the measurements is 1.1 million years, assuming that this was preceded by more than 280,000 years of ice-free conditions. Other scenarios, in which Greenland was ice-free during any or all Pleistocene interglacials, may be more realistic. Our observations are incompatible with most existing model simulations that present a continuously existing Pleistocene GIS. Future simulations of the GIS should take into account that Greenland was nearly ice-free for extended periods under Pleistocene climate forcing.