The effect of the fault rupture zone traversing a seismically isolated bridge is investigated utilizing a finite element model of a section of the Bolu Viaduct and a set of synthetic broadband strong ground motions simulated for the Bolu Viaduct site due to the 1999 Duzce earthquake. Both the original and a potential retrofit seismic isolation system designs are considered in the analyses. The results show double isolation system demands when fault crossing is considered, as compared to the case where fault crossing is ignored. The pier drift demands, however, remain comparable in both cases. Furthermore, the location of fault crossing along the bridge length, as well as the fault orientation with respect to the bridge longitudinal direction are shown to influence substantially the response of the seismically isolated bridge. Isolation system permanent displacements are greatly influenced by the restoring force capability of the isolation system when fault crossing effects in the excitations are ignored. In the case of fault crossing, the permanent displacements of the isolation system are dominated by the substantial permanent tectonic displacement along the fault trace which is imposed upon the structure. The results of this study contribute to developing a better understanding of how seismically isolated bridges respond when traversed by fault rupture zones. The lack of analyses and design guidelines for bridges crossing faults in international standards renders this study a useful reference for the profession.