Conditional spectra (CS) are applied to the seismic fragility assessment of a nuclear power plant (NPP) containment building for comparison with a relevant conventional uniform hazard response spectrum (UHRS). Three different control frequencies are considered in developing conditional spectra. The contribution of diverse magnitudes and epicentral distances is identified from deaggregation for the UHRS at a control frequency and incorporated into the conditional spectra. A total of 30 ground motion records are selected and scaled to simulate the probability distribution of each conditional spectra, respectively. A set of lumped mass stick models for the containment building are built considering nonlinear bending and shear deformation and uncertainty in modeling parameters using the Latin hypercube sampling technique. Incremental dynamic analysis is conducted for different seismic input models in order to estimate seismic fragility functions. The seismic fragility functions and high confidence of low probability of failure (HCLPF) are calculated for different seismic input models and analyzed comparatively.