In today’s world of falling returns on fixed exploration budgets, complex targets, and ever-increasing volumes of multi-parameter datasets, the effective management and integration of existing data are essential to any mineral exploration operation. Machine learning (ML) algorithms like Convolutional Neural Networks (CNN), Random Forest (RF), and Support Vector Machine (SVM) are powerful data-driven methods that are not implemented very often with remote sensing-derived hydrothermal alternation information and limited field datasets for mapping mineral prospectivity. The application of machine learning algorithms with satellite remote sensing data and limited field data, they have not been compared and evaluated together thoroughly in this field. A data science approach was applied to create nine predictor maps, incorporating limited field data and satellite remote sensing information. A confusion matrix, statistical measures, and a Receiver Operating Characteristic (ROC) curve were used to evaluate the prediction models efficacy on both the training and test datasets. The results suggested that the RF model exhibited the highest predictive accuracy, consistency and interpretability among the three ML models evaluated in this study. RF model also achieved the highest predictive efficiency in capturing known copper (Cu) deposits within a small prospective area. In comparison to the SVM and CNN models, the RF model outperformed them in terms of predictive accuracy and interpretability. These results imply that the RF model is the most suitable for Cu potential mapping in the Pakistan’s North Waziristan region. Consequently, all the models including the RF model were used to generate a prospectivity map, which contained low to very-high potential zones, to support further exploration in the region. The newly discovered deposit inside the predicted prospective areas demonstrates the robustness and efficacy of the prospectivity modelling approach as proposed in this research for generating exploration targets.