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Abstract Geomagnetic storms can cause variations in the ionization levels of the ionosphere, which is commonly studied using the total electron content (TEC). TEC is a crucial parameter to identify the possible effects of ionospheric variations on satellite communication and navigation. This paper assesses the performance of light gradient boosting machine (LGB) and deep neural network (DNN) machine learning algorithms in modeling ionospheric vertical TEC (VTEC) during geomagnetic disturbances. GPS VTEC data for years 2011–2016 from 13 dual-frequency receiver stations over Ethiopia was utilized. Input parameters for the models were derived from the factors that influence VTEC, such as time, location, geomagnetic activity, solar activity, solar wind, and the interplanetary magnetic field. The LGB model improved the predictions of the DNN model from root mean squared error (RMSE), mean absolute percentage error (MAPE), and R2 values of 5.45 TECU, 21%, and 0.93 to 4.98 TECU, 18%, and 0.94 on the testing data, respectively. The two machine learning models significantly outperformed the International Reference Ionosphere (IRI 2020) model during the selected geomagnetic storm periods. This study could provide insight into the impacts of ionosphere variations on satellite communication and navigation systems in the low-latitude ionospheric region.