In this study, a three-dimensional finite element model of the Bill Emerson Memorial cable-stayed bridge was developed and validated with the acceleration data recorded during the M4.1 earthquake of May 1, 2005, in Manila, Arkansas. The model took into account the geometric nonlinear properties associated with cable sagging and soil-foundation-structure interaction. The validated model was used to evaluate the performance of a seismic protective system, the behavior of cable-stayed spans, and the accuracy of two simplified bridge models that have been extensively used by the structural control community. The calculated natural frequencies and mode shapes correlated well with the measured data. Except that the hollow columns of two H-shaped towers were near yielding immediately above their capbeams, the cable-stayed spans behaved elastically as expected under the design earthquake that was scaled up from the recorded rock motions at the bridge site. The minimum factor of safety of all cables is 2.78, which is slightly greater than the design target.