Abstract.A considerable fraction of the solar wind energy that crosses the magnetopause ends up in the high-latitude thermosphere-ionosphere system as a result of Joule heating, the consequences of which are very significant and global in nature. Often Joule heating calculations use hourly averages of the electric field, rather than the time-varying electric field. This leads to an underestimation of the heating. In this paper, we determine the magnitude of the underestimation of Joule heating by analysing electric field data from the EISCAT Incoherent Scatter Radar, situated at the 67 • E magnetic latitude. We find that the underestimation, using hourly-averaged electric field values, is normally ∼20%, with an upper value of about 65%. We find that these values are insensitive to changes in solar flux, magnetic activity and magnetic local time, implying that the electric field fluctuations are linear related to the amplitude of the electric field. Assuming that these changes are representative of the entire auroral oval, we then use a coupled ionosphere-thermosphere model to calculate the local changes these underestimations in the heating rate cause to the neutral temperature, mean molecular mass and meridional wind. The changes in each parameter are of the order of a few percent but they result in a reduction in the peak F-region concentration of ∼20% in the summer hemisphere at high latitudes, and about half of this level in the winter hemisphere. We suggest that these calculations could be used to add corrections to modelled values of Joule heating.