Rare earth elements (REEs), a significant subset of critical minerals, play an indispensable role in modern society and are regarded as “industrial vitamins,” making them crucial for global sustainability. Geochemical survey data proves highly effective in delineating metallic mineral prospects. Separating geochemical anomalies associated with specific types of mineralization from the background reflecting geological processes has long been a significant subject in exploration geochemistry. The processing of high-dimensional, non-linear geochemical survey data necessitates a systematic framework to address common issues, including missing values, the closure effect, the selection of appropriate multivariate analysis methods, and anomaly detection techniques in order to detect geochemical anomalies associated with mineral occurrences. The Curnamona Province in South Australia is considered an emerging REE province with significant REE mineralization potential. In this study, we use data from this region to evaluate the performance of a novel machine learning-based framework that incorporates data pre-processing, multivariate statistical analysis, and anomaly recognition to address challenges such as missing data, noise interference, data imbalance and high non-linearity. We utilize lithogeochemical data to map potential greenfield regions of REE mineralization. The primary advantages of our framework lie in its provision of an effective random forest-based data imputation method, utilization of isometric log-ratio transformation to eliminate the closure effect, and reduction of the impact of outliers on data interpretation through robust principal component analysis. Additionally, the framework utilizes a deviation network to learn anomaly scores from complex, non-linear data under imbalanced data conditions, identifying geochemical anomalies associated with REE occurrences by leveraging prior knowledge rather than those caused by data noise or anthropogenic factors. The anomalous areas identified by this framework delineate all known REE deposits and extend to the surrounding regions. Furthermore, a close spatial coupling relationship exists between these strongly anomalous areas and the felsic granite intrusions. The comprehensive workflow for processing geochemical data proposed in this study can effectively address common challenges in the geochemical exploration of critical minerals. The identified geochemical anomalies can provide important clues for subsequent exploration.