One of the important causes of building and infrastructure failure, such as bridges on pile foundations, is the placement of the piles in liquefiable soil that can become unstable under seismic loads. Therefore, the overarching aim of this study is to investigate the seismic behavior of a soil-pile system in liquefiable soil using three-dimensional numerical FEM analysis, including soil-pile interaction. Effective parameters on concrete pile response, involving the pile diameter, pile length, soil type, and base acceleration, were considered in the framework of finite element non-linear dynamic analysis. The constitutive model of soil was considered as elasto-plastic kinematic-isotropic hardening. First, the finite element model was verified by comparing the variations on the pile response with the measured data from the centrifuge tests, and there was a strong agreement between the numerical and experimental results. Totally 64 non-linear time-history analyses were conducted, and the responses were investigated in terms of the lateral displacement of the pile, the effect of the base acceleration in the pile behavior, the bending moment distribution in the pile body, and the pore pressure. The numerical analysis results demonstrated that the relationship between the pile lateral displacement and the maximum base acceleration is non-linear. Furthermore, increasing the pile diameter results in an increase in the passive pressure of the soil. Also, piles with small and big diameters are subjected to yielding under bending and shear states, respectively. It is concluded that an effective stress-based ground response analysis should be conducted when there is a liquefaction condition in order to determine the maximum bending moment and shear force generated within the pile.