The geothermal heat flux is a critical thermal boundary condition that influences the melting, flow, and mass balance of ice sheets, but measurements of this parameter are difficult to make in ice-covered regions. We report the first direct measurement of geothermal heat flux into the base of the West Antarctic Ice Sheet (WAIS), below Subglacial Lake Whillans, determined from the thermal gradient and the thermal conductivity of sediment under the lake. The heat flux at this site is 285 ± 80 mW/m2, significantly higher than the continental and regional averages estimated for this site using regional geophysical and glaciological models. Independent temperature measurements in the ice indicate an upward heat flux through the WAIS of 105 ± 13 mW/m2. The difference between these heat flux values could contribute to basal melting and/or be advected from Subglacial Lake Whillans by flowing water. The high geothermal heat flux may help to explain why ice streams and subglacial lakes are so abundant and dynamic in this region.