This study aims to examine three machine learning (ML) techniques, namely random forest (RF), LightGBM, and CatBoost for flooding susceptibility maps (FSMs) in the Vietnamese Vu Gia-Thu Bon (VGTB). The results of ML are compared with those of the rainfall-runoff model, and different training dataset sizes are utilized in the performance assessment. Ten independent factors are assessed. An inventory map with approximately 850 flooding sites is based on several post-flood surveys. The inventory dataset is randomly split between training (70%) and testing (30%). The AUC-ROC results are 97.9%, 99.5%, and 99.5% for CatBoost, LightGBM, and RF, respectively. The FSMs developed by the ML methods show good agreement in terms of an extension with flood inundation maps developed using the rainfall-runoff model. The models’ FSMs showed 10–13% of the total area to be highly susceptible to flooding, consistent with RRI’s flood map. The FSMs show that downstream areas (both urbanized and agricultural) are under high and very high levels of susceptibility. Additionally, different sizes of the input datasets are tested to determine the least number of data points having acceptable reliability. The results demonstrate that the ML methods can realistically predict FSMs, regardless of the number of training samples.