Display omitted •Novel machine learning-based framework for exploring critical mineral deposits.•Improved generative adversarial network for data augmentation.•Prospectivity maps show a strong correlation with known mineral occurrences.•Models outperform standard random forest classifier.•Geophysical features crucial in mapping prospective critical mineral regions. The demand for critical minerals is rapidly increasing worldwide, yet future global supply remains uncertain due to the difficulty in discovering new deposits using traditional methods. To increase the success rate of exploration projects for these vital resources, the use of artificial intelligence is continuously increasing for big and complex data analysis. This study proposes a new machine learning-based framework that tackles common problems associated with exploring critical mineral deposits, such as the shortage of known mineral occurrences, challenges in selecting negative samples in barren regions, and unbalanced training data. Our framework combines an improved generative adversarial network with positive and unlabelled learning to enhance efficiency. To test the performance of the framework, we create prospectivity maps of mafic–ultramafic intrusion-hosted mineralisation for cobalt, chromium, and nickel in the Gawler Craton, South Australia. The models are trained on a carefully selected set of independent features based on a conceptual model derived from open-access exploration data, resulting in high and stable performance. The prospectivity maps show a strong spatial correlation between high probabilities and known mineral occurrences and predict potential greenfield regions for future exploration. Our models demonstrate a significantly higher accuracy compared to a conventional approach using a standard random forest classifier and reveal that geophysical features play a crucial role in mapping prospective regions of critical minerals. Overall, our framework has the potential to significantly enhance critical mineral exploration by providing a more accurate and efficient approach to identifying prospective regions for future mining operations.