Numerical dynamo models have been successful in explaining the origin of the Earth's magnetic field and its secular variation by convection in the electrically conducting fluid outer core1,2,3,4,5,6,7. An important component of the convection in the numerical dynamos are polar vortices beneath the core–mantle boundary in each hemisphere. These polar vortices in the outer core have been proposed as sources for both the anomalous rotation of the inner core and the toroidal part of the geomagnetic field2,8. Here we use the observed structure of the Earth's magnetic field and its variation since 1870 to infer the existence of an anticyclonic polar vortex with a polar upwelling in the northern hemisphere of the core, consistent with the polar vortices found in numerical dynamos.