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Current studies lack probabilistic evaluations on the performance of fault-crossing bridges. This paper conducts seismic fragility analyses to evaluate the fragility of cable-stayed bridges with the effects of fault ruptures. Synthetic across-fault ground motions are generated using existing simulation methods for the low-frequency pulses and high-frequency residuals. Incremental dynamic analysis is utilized to generate the seismic responses of the bridge. The optimal intensity measure (IM) for a cable-stayed bridge that crosses a fault is identified based on the coefficient of determination (<i>R</i>²). Root-mean-square velocity (V_rms) is found to be the best IM for cable-stayed bridges traversed by fault ruptures, instead of the commonly used ones such as peak ground acceleration or velocity (PGA or PGV). Fragility curves for the critical components of fault-crossing cable-stayed bridges, including pylons, cables, and bearings, are developed using the IM of V_rms, and are subsequently compared with those for the cable-stayed bridge near faults. Results show that the bearings on transition piers are the most vulnerable component for fault-crossing cable-stayed bridges because of the rotation of their girder. Compared to cable-stayed bridges near faults, pylons and bearings are more vulnerable in the transverse direction for cable-stayed bridges crossing faults, whereas the vulnerability of cables is comparable.