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Background Emergency Department (ED) overcrowding is an emerging risk to patient safety. This study aims to assess and compare the predictive ability of machine learning (ML) models for predicting frequent ED users. Method Korean Health Panel data from 2008 to 2015 were used for this study. Individuals with four or more visits per year were considered frequent ED users. Logistic Regression (LR), Random Forest (RF), Support Vector Machine (SVM) as well as two ensemble models, namely Bagging and Voting, were trained and tested to examine their predictive performance. Results The ML classification algorithms identified frequent ED users with high precision (90%–98%) and sensitivity (87%–91%), whereas LR showed fair precision (65%) and sensitivity (67%). The ML algorithms showed a high area under the curve (AUC) values from 89% for SVM to 96% for Random Forest, while LR showed the lowest AUC (65%). The classification error varied among algorithms; LR had the highest classification error (24.07%) while RF had the least (3.8%). Conclusions Results show that ML classification algorithms are robust techniques to predict frequent ED users, and the variables in administrative health panels are reliable indicators for this purpose.