This paper investigates the dynamic response of a model pile-soil-bridge system subjected to seismic loading using a finite element model (FEM) developed in OpenSees. The numerical model is validated against shake table test data from a companion experimental study, which tested a piles-bridge model fabricated from organic glass. The bridge model comprised four piers, each supported by two-by-two pile groups, with edge piers featuring 60 × 60 mm rubber pads between the pier and deck. Two earthquake ground motions, El Centro and Tianjin, were applied at three intensity levels. The calculated and measured responses show good agreement. The validated FEM reveals that the El Centro earthquake typically induces higher acceleration and moment responses in structural elements compared to the Tianjin earthquake, while the Tianjin earthquake results in greater displacement responses. These findings highlight the impact of earthquake wave characteristics, such as predominant period, on the bridge system's response. Furthermore, the bending moments at the pier top for edge piers remain relatively consistent across different earthquake motions and intensity levels, indicating the role of rubber pads in mitigating seismic forces in the piers.