AbstractMost recent methods in ionospheric tomography are based on the inversion of the total electron content measured by ground‐based GPS receivers. As a consequence of the high frequency of the GPS signal and the absence of horizontal raypaths, the electron density structure is mainly reconstructed in the F2 region (300 km), where the ionosphere reaches the maximum of ionization, and is not sensitive to the lower ionospheric structure. We propose here a new tomographic method of the lower ionosphere, based on the full inversion of over‐the‐horizon (OTH) radar data. Previous studies using OTH radar for ionospheric tomography inverted only the leading edge echo curve of backscatter ionograms. The major advantage of our methodology is taking into account, numerically and jointly, the effect that the electron density perturbations induce not only in the speed of electromagnetic waves but also on the raypath geometry. This last point is extremely critical for OTH radar inversions as the emitted signal propagates through the ionosphere between a fixed starting point (the radar) and an unknown end point on the Earth surface where the signal is backscattered. We detail our ionospheric tomography method with the aid of benchmark tests. Having proved the necessity to take into account both effects simultaneously, we apply our method to real data. This is the first time that the effect of the raypath deflection has been quantified and that the ionospheric plasma density has been estimated over the entirety of Europe with an OTH radar.