This study focuses on the prediction of concrete cover separation (CCS) in reinforced concrete beams strengthened by fiber-reinforced polymer (FRP) in flexure. First, machine learning models were constructed based on linear regression, support vector regression, BP neural networks, decision trees, random forests, and XGBoost algorithms. Secondly, the most suitable model for predicting CCS was identified based on the evaluation metrics and compared with the codes and the researcher’s model. Finally, a parametric study based on SHapley Additive exPlanations (SHAP) was carried out, and the following conclusions were obtained: XGBoost is best-suited for the prediction of CCS and codes, and researchers’ model accuracy needs to be improved and suffers from over or conservative estimation. The contributions of the concrete to the shear force and the yield strength of the reinforcement are the most important parameters for the CCS, where the shear force at the onset of CCS is approximately proportional to the contribution of the concrete to the shear force and approximately inversely proportional to the yield strength of the reinforcement.