Although advanced modeling techniques such as the finite element method (FEM) have been used successfully in dynamic site response analysis, the high computational expense has hindered the incorporation of uncertainty analysis. In this paper, the RSM surrogate model was implemented in the context of seismic site response analysis to evaluate the uncertainty of the PGA due to the propagation of input parameter uncertainty. To derive the RSM model, a parametric study of the dynamic site responses using FEM code ABAQUS with the modified Davidenkov soil constitutive model is conducted. The input parameters, including the soil profile, soil properties, and input ground motion are then characterized and screened for their suitability to be included in the RSM model. For a given site response problem, representative “samples” are taken for site response analysis using ABAQUS, and the response surface is constructed using the outcomes of the numerical experimentations. The accuracy of the developed RSM model is then validated. Once the RSM model is deemed satisfactory, the reliability-based formulation for evaluating the mean and standard deviation of the surface PGA is established. Example is provided to illustrate the RSM approach for dynamic site response analysis in the face of input parameter uncertainty.