Carbonatites are the primary geological sources for rare earth elements (REEs) and niobium (Nb). This study applies machine learning techniques to generate national-scale prospectivity models and support mineral exploration targeting of Canadian carbonatite-hosted REE +/− Nb deposits. Extreme target feature label imbalance, diverse geological settings hosting these deposits throughout Canada, selecting negative labels, and issues regarding the interpretability of some machine learning models are major challenges impeding data-driven prospectivity modeling of carbonatite-hosted REE +/− Nb deposits. A multi-stage framework, exploiting global hierarchical tessellation model systems, data-space similarity measures, ensemble modeling, and Shapley additive explanations was coupled with convolutional neural networks (CNN) and random forest to meet the objectives of this work. A risk–return analysis was further implemented to assist with model interpretation and visualization. Multiple models were compared in terms of their predictive ability and their capability of reducing the search space for mineral exploration. The best-performing model, derived using a CNN that incorporates public geoscience datasets, exhibits an area under the curve for receiver operating characteristics plot of 0.96 for the testing labels, reducing the search area by 80%, while predicting all known carbonatite-hosted REE +/− Nb occurrences. The framework used in our study allows for an explicit definition of input vectors and provides a clear interpretation of outcomes generated by prospectivity models.