Low Earth orbit satellites collect and study information on changes in the ionosphere, which contributes to the identification of earthquake precursors. Swarm, the European Space Agency three-satellite mission, has been launched to monitor the Earth geomagnetic field, and has successfully shown that in some cases it is able to observe many several ionospheric perturbations that occurred as a result of large earthquake activity. This paper proposes the SafeNet deep learning framework for detecting pre-earthquake ionospheric perturbations. We trained the proposed model using 9017 recent (2014–2020) independent earthquakes of magnitude 4.8 or greater, as well as the corresponding 7-year plasma and magnetic field data from the Swarm A satellite, and excellent performance has been achieved. In addition, the influence of different model inputs and spatial window sizes, earthquake magnitudes, and daytime or nighttime was explored. The results showed that for electromagnetic pre-earthquake data collected within a circular region of the epicenter and with a Dobrovolsky-defined radius and input window size of 70 consecutive data points, nighttime data provided the highest performance in discriminating pre-earthquake perturbations, yielding an F1 score of 0.846 and a Matthews correlation coefficient of 0.717. Moreover, SafeNet performed well in identifying pre-seismic ionospheric anomalies with increasing earthquake magnitude and unbalanced datasets. Hypotheses on the physical causes of earthquake-induced ionospheric perturbations are also provided. Our results suggest that the performance of pre-earthquake ionospheric perturbation identification can be significantly improved by utilizing SafeNet, which is capable of detecting precursor effects within electromagnetic satellite data.