Tropospheric thunderstorms have been reported to disturb the lower ionosphere, at altitudes of 65–90 km, by convective atmospheric gravity waves^,,,, and by electric field changes produced by lightning discharges^,,,,,,,,,. Theoretical simulations suggest that lightning electric fields enhance electron attachment to O₂ and reduce electron density in the lower ionosphere^,. Owing to the low electron density in the lower ionosphere, active probing of its electron distribution is difficult^,, and the various perturbative effects are poorly understood. However, it is now possible to probe the lower ionosphere in a spatially and temporally resolved manner by using remotely detected time waveforms of lightning radio signals^,,,. Here we report such observations of the night-time ionosphere above a small thunderstorm. We find that electron density in the lower ionosphere decreased in response to lightning discharges. The extent of the reduction is closely related in time and space to the rate of lightning discharges, supporting the idea that the enhanced electron attachment is responsible for the reduction. We conclude that ionospheric electron density variations corresponding to lightning discharges should be considered in future simulations of the ionosphere and the initiation of sprite discharges.