This research aims to study the seismic fragility evaluations of slender piers with single-column sections on prestressed concrete viaducts to investigate how pier height, prestressing force, and ground motion intensity are related, not only in terms of mean values but also in their probability density functions (PDFs), which inherently imply parameters such as dispersion indices. A detailed nonlinear numerical analysis was performed using a finite element model that incorporated the realistic response of concrete, steel, and infrm-FB element types for the columns. To this end, fragility curves were developed based on a probabilistic procedure that accounted for the variability of material properties, pier geometry, and seismic loading. The results show that the fragility function of high piers is hardly dependent on the shear span efficiency. Conversely, slender piers exhibit an increased level of fragility when the effect is confined to a constant prestressing force. This study highlights the need to account for the nonlinearity of pier members and variation in seismic loading when estimating the seismic fragility of slender piers. The conclusions of this study are beneficial for designing and retrofitting strategies for prestressed concrete viaducts in seismic regions.