The aim of this study is to investigate the role of [18F]-PSMA-1007 PET in differentiating high- and low-risk prostate cancer (PCa) through a robust radiomics ensemble model. This retrospective study included 143 PCa patients who underwent [18F]-PSMA-1007 PET/CT imaging. PCa areas were manually contoured on PET images and 1781 image biomarker standardization initiative (IBSI)-compliant radiomics features were extracted. A 30 times iterated preliminary analysis pipeline, comprising of the least absolute shrinkage and selection operator (LASSO) for feature selection and fivefold cross-validation for model optimization, was adopted to identify the most robust features to dataset variations, select candidate models for ensemble modelling, and optimize hyperparameters. Thirteen subsets of selected features, 11 generated from the preliminary analysis plus two additional subsets, the first based on the combination of robust and fine-tuning features, and the second only on fine-tuning features were used to train the model ensemble. Accuracy, area under curve (AUC), sensitivity, specificity, precision, and f-score values were calculated to provide models’ performance. Friedman test, followed by post hoc tests corrected with Dunn-Sidak correction for multiple comparisons, was used to verify if statistically significant differences were found in the different ensemble models over the 30 iterations. The model ensemble trained with the combination of robust and fine-tuning features obtained the highest average accuracy (79.52%), AUC (85.75%), specificity (84.29%), precision (82.85%), and f-score (78.26%). Statistically significant differences (p < 0.05) were found for some performance metrics. These findings support the role of [18F]-PSMA-1007 PET radiomics in improving risk stratification for PCa, by reducing dependence on biopsies.