This study attempts to investigate the influence of the dynamic soil properties uncertainties on ground response analysis via a case study site. For this purpose, nonlinear time-domain ground response analysis and uncertainties in soil parameters are coupled simultaneously using a coded program in MATLAB. To take full advantage of the real data, two investigation boreholes are drilled in the site. The analysis is performed deterministically and then extended to the stochastic context in order to take into consideration the variability of Plastic Index, shear wave velocity, and unit weight of the soil. In a part of this study, the capability of the three different methods for predicting the stochastic fundamental period of the site including modal analysis, approximate method, and nonlinear method, is investigated. To achieve the advantage of the stochastic analysis, the maximum Coefficient of Variation (COV) of the peak ground motion parameters, fundamental period, response spectrum, and amplification factor are calculated. The results demonstrate that the heterogeneity of the soil parameters has a significant effect on the variation of the surface Peak Ground Displacement (PGD). Among the other stochastic responses, the fundamental period has received the least effect from soil parameters’ uncertainty.