Geothermal heat flux (GHF) is an important part of the basal heat budget of continental ice sheets. The difficulty of measuring GHF below ice sheets has directly hindered progress in understanding of ice sheet dynamics. We present a new GHF measurement from below the West Antarctic Ice Sheet, made in subglacial sediment near the grounding zone of the Whillans Ice Stream. The measured GHF is 88 ± 7 mW m-2, a relatively high value compared to other continental settings and to other GHF measurements along the eastern Ross Sea of 55 mW m-2 and 69 ± 21 mW m-2, but within the range of regional values indicated by geophysical estimates. The new GHF measurement was made ~100 km from the only other direct GHF measurement below the ice sheet, which was considerably higher at 285 ± 80 mW m-2, suggesting spatial variability that could be explained by shallow magmatic intrusions or the advection of heat by crustal fluids. Analytical calculations suggest that spatial variability in GHF exceeds spatial variability in the conductive heat flux through ice along the Siple Coast. Accurate GHF measurements and high-resolution GHF models may be necessary to reliably predict ice sheet evolution, including responses to ongoing and future climate change.