Prestressed concrete composite girder bridges with corrugated steel webs (PCCGBCSWs) are extensively employed in bridge construction because of their low dead weight, fast construction, and high prestressing efficiency. Moreover, PCCGBCSWs will experience deformation and failure of the corrugated steel webs, including steel fatigue and fracture, during earthquakes. These changes will introduce safety hazards, which can be addressed via bridge disaster prevention and mitigation. Because near-fault pulse-like ground motions (NFPLGMs) have high peak accelerations, these motions can easily cause damage to a bridge. Therefore, in this study, a seismic fragility assessment is performed for long-unit PCCGBCSWs subjected to NFPLGMs considering spatial variability effects, and a sensitivity evaluation of the seismic fragility is conducted considering girder type, bearing type, ground motion type, and apparent wave velocity to offer a point of reference for seismic design. The results show that PCCGBCSWs are less vulnerable than concrete bridges. The shock absorption effect of the friction pendulum bearing is better than that of the viscous damper. The impact of NFPLGMs on bridges is greater than that of near-fault non-pulse-like ground motions (NFNPLMs) and far-fault ground motions (FFGMs). The seismic fragility under nonuniform excitation conditions is greater than that under uniform excitation conditions, showing an increasing trend with decreasing apparent wave velocity.