Ionospheric scintillation is a pressing issue in space weather studies due to its diverse effects on positioning, navigation, and timing (PNT) systems. Developing an accurate and timely prediction model for this event is crucial. In this work, we developed two machine learning models for the prediction of ionospheric scintillation events at the equatorial anomaly during the maximum and minimum phases of solar cycle 24. The models developed in this study are the Random Forest (RF) algorithm and the eXtreme Gradient Boosting (XGBoost) algorithm. The models take inputs based on the solar wind parameters obtained from the OMNI Web database from the years 2010–2017 and Pc5 wave power obtained from the Bear Island (BJN) magnetometer station. We retrieved data from the Scintillation Network and Decision Aid (SCINDA) receiver in Egypt from which the S4 index was computed to quantify amplitude scintillations that were utilized as the target in the model development. Out-of-sample model testing was performed to evaluate the prediction accuracy of the models on unseen data after training. The similarity between the observed and predicted scintillation events, quantified by the R2 score, was 0.66 and 0.74 for the RF and XGBoost models, respectively. The corresponding Root Mean Square Errors (RMSEs) associated with the models were 0.01 and 0.01 for the RF and XGBoost models, respectively. The similarity in error shows that the XGBoost model is a good and preferred choice for the prediction of ionospheric scintillation events at the equatorial anomaly. With these results, we recommend the use of ensemble learning techniques for the study of the ionospheric scintillation phenomenon.