The permeability coefficient (k) of soil is one of the most important parameters affecting soil characteristics such as shear strength or settlement. Thus, determining soil permeability coefficient is very crucial; however, a field test for determining this parameter is difficult, time-consuming, and expensive. In this study, soft computing methods, namely, M5P and Gaussian process (GP), for estimating the permeability coefficient were constructed and compared. The results of this paper indicate that the two soft computing algorithms functioned well in predicting k. These two methods gave high accuracy of prediction capability. The determination coefficient of M5P (R2 = 0.766) was higher than that (R2 = 0.700) of GP. This implies that the M5P model is more reliable estimation than the GP model in predicting soils’ permeability coefficient (k). This proves that applying these machine learning techniques can provide an alternative for predicting basic soil parameters, including the permeability coefficient of soil.