Helium is used as a critical tracer throughout the Earth sciences, where its relatively simple isotopic systematics is used to trace degassing from the mantle, to date groundwater and to time the rise of continents(1). The hydrothermal system at Yellowstone National Park is famous for its high helium-3/helium-4 isotope ratio, commonly cited as evidence for a deep mantle source for the Yellowstone hotspot(2). However, much of the helium emitted from this region is actually radiogenic helium-4 produced within the crust by alpha-decay of uranium and thorium. Here we show, by combining gas emission rates with chemistry and isotopic analyses, that crustal helium-4 emission rates from Yellowstone exceed (by orders of magnitude) any conceivable rate of generation within the crust. It seems that helium has accumulated for (at least) many hundreds of millions of years in Archaean (more than 2.5 billion years old) cratonic rocks beneath Yellowstone, only to be liberated over the past two million years by intense crustal metamorphism induced by the Yellowstone hotspot. Our results demonstrate the extremes in variability of crustal helium efflux on geologic time-scales and imply crustal-scale open-system behaviour of helium in tectonically and magmatically active regions.