Accurate reservoir permeability determination is crucial in hydrocarbon exploration and production. Conventional methods relying on empirical correlations and assumptions often result in high costs, time consumption, inaccuracies, and uncertainties. This study introduces a novel hybrid machine learning approach to predict the permeability of the Wangkwar formation in the Gunya oilfield, Northwestern Uganda. The group method of data handling with differential evolution (GMDH-DE) algorithm was used to predict permeability due to its capability to manage complex, nonlinear relationships between variables, reduced computation time, and parameter optimization through evolutionary algorithms. Using 1953 samples from Gunya-1 and Gunya-2 wells for training and 1563 samples from Gunya-3 for testing, the GMDH-DE outperformed the group method of data handling (GMDH) and random forest (RF) in predicting permeability with higher accuracy and lower computation time. The GMDH-DE achieved an R2 of 0.9985, RMSE of 3.157, MAE of 2.366, and ME of 0.001 during training, and for testing, the ME, MAE, RMSE, and R2 were 1.3508, 12.503, 21.3898, and 0.9534, respectively. Additionally, the GMDH-DE demonstrated a 41% reduction in processing time compared to GMDH and RF. The model was also used to predict the permeability of the Mita Gamma well in the Mandawa basin, Tanzania, which lacks core data. Shapley additive explanations (SHAP) analysis identified thermal neutron porosity (TNPH), effective porosity (PHIE), and spectral gamma-ray (SGR) as the most critical parameters in permeability prediction. Therefore, the GMDH-DE model offers a novel, efficient, and accurate approach for fast permeability prediction, enhancing hydrocarbon exploration and production.