Consideration of uncertainty is crucial in hazardous structures, such as nuclear power plants subjected to seismic loading. It is expected that taking into account the uncertainty of several parameters involved in the analysis would provide more reliable and stable results, however the computational time might increase considerably depending on the structural numerical model and analysis methods. In this paper, we compare the fragility curves using different analysis methods for 3-D finite element model and a simplified 1-D finite element model of a reinforced concrete test structure from a previous research project. The 3-D finite element model developed is analyzed considering linear and nonlinear material properties subjected to dynamic loading. Using the simplified model, the fragility curves are obtained considering the uncertainty in ground motion, material properties, and in boundary conditions. Response surface methods are utilized for probabilistic computation.