As the rate of percutaneous coronary intervention increases, in-stent restenosis (ISR) has become a burden. Random forest (RF) could be superior to logistic regression (LR) for predicting ISR due to its robustness. We developed an RF model and compared its performance with the LR one for predicting ISR. We retrospectively included 1501 patients (age: 64.0 ± 10.3; male: 76.7%; ISR events: 279) who underwent coronary angiography at 9 to 18 months after implantation of 2nd generation drug-eluting stents. The data were randomly split into a pair of train and test datasets for model development and validation with 50 repeats. The predictive performance was assessed by the area under the curve (AUC) of the receiver operating characteristic (ROC). The RF models predicted ISR with larger AUC-ROCs of 0.829 ± 0.025 compared to 0.784 ± 0.027 of the LR models. The difference was statistically significant in 29 of the 50 repeats. The RF and LR models had similar sensitivity using the same cutoff threshold, but the specificity was significantly higher in the RF models, reducing 25% of the false positives. By removing the high leverage outliers, the LR models had comparable AUC-ROC to the RF models. Compared to the LR, the RF was more robust and significantly improved the performance for predicting ISR. It could cost-effectively identify patients with high ISR risk and help the clinical decision of coronary stenting.