© 2022, The Author(s), under exclusive licence to International Skeletal Society (ISS).Objective: To assess the diagnostic performance of MRI-based texture analysis for differentiating enchondromas and chondrosarcomas, especially on fat-suppressed proton density (FS-PD) images. Materials and methods: The whole tumor volumes of 23 chondrosarcomas and 24 enchondromas were manually segmented on both FS-PD and T1-weighted images. A total of 861 radiomic features were extracted. SelectKBest was used to select the features. The data were randomly split into training (n = 36) and test (n = 10) for T1-weighted and training (n = 37) and test (n = 10) for FS-PD datasets. Fivefold cross-validation was performed. Fifteen machine learning models were created using the training set. The best models for T1-weighted, FS-PD, and T1-weighted + FS-PD images were selected in terms of accuracy and area under the curve (AUC). Results: There were 7 men and 16 women in the chondrosarcoma group (mean ± standard deviation age, 45.65 ± 11.24) and 7 men and 17 women in the enchondroma group (mean ± standard deviation age, 46.17 ± 11.79). Naive Bayes was the best model for accuracy and AUC for T1-weighted images (AUC = 0.76, accuracy = 80%, recall = 80%, precision = 80%, F1 score = 80%). The best model for FS-PD images was the K neighbors classifier for accuracy and AUC (AUC = 1.00, accuracy = 80%, recall = 80%, precision = 100%, F1 score = 89%). The best model for T1-weighted + FS-PD images was logistic regression for accuracy and AUC (AUC = 0.84, accuracy = 80%, recall = 60%, precision = 100%, F1 score = 75%). Conclusion: MRI-based machine learning models have promising results in the discrimination of enchondroma and chondrosarcoma based on radiomic features obtained from both FS-PD and T1-weighted images.