A growing global health concern, non-alcoholic fatty liver disease (NAFLD) must be accurately and promptly detected to avoid serious complications. This study suggests a model based on Natural Gradient Boosting (NGBoost) for accurate clinical feature-based NAFLD prediction. In contrast to traditional gradient boosting algorithms, NGBoost uses natural gradients to estimate the entire conditional probability distribution of outcomes, which enhances uncertainty quantification and calibration. Using a publicly accessible Kaggle dataset, the model’s performance was compared to KNN, SVM, and Decision Tree classifiers. According to experimental results, NGBoost outperformed conventional classifiers in terms of precision, recall, and F1 score, achieving the highest accuracy of 92.8%. Excellent discriminative ability was indicated by the ROC curve, and strong generalization ability with minimal overfitting was confirmed by the training–validation loss analysis. These findings demonstrate how NGBoost may be used to support clinical decisions, allowing for earlier detection and treatment. Subsequent research endeavors will investigate the validation of the model on more extensive real-world datasets and broaden its relevance to additional liver-related conditions.