This paper uses the fragility function method to study the effects of pounding and skewness on the seismic behaviors of typical multispan RC highway bridges. Three-dimensional numerical models are built for typical three-span bridges in California that include nonlinear pier columns, distributed gap elements simulating pounding at both expansion joints and end abutments, and soil-structure interaction effects. The spatial differences of seismic excitations at various supports caused by varied soil profile properties and wave propagation effects, etc., are also included. As indicated by the nonlinear time history analyses using a large set of three-component earthquake ground motion records, fragility functions are derived and compared for bridges with various structural details, including the location of gaps, deck skew angle, and gap size. Although pounding causes significant local damage, the fragility functions show relatively moderate change in damage probability of the entire bridge. When pounding does not happen, skewed bridges outperform straight ones because of their coupled responses. For straight bridges, the pounding has a limited effect on bridge level damage and can be negligible. However, pounding results in increased damages of skewed bridges which aggravate with large skew angles. Using fragility functions, this paper clarifies the interactive roles of skewness and pounding for seismic damage probability of multispan highway bridges. These findings can provide valuable guidance for future bridge design.