Seismic performance of critical facilities has been focused on the structural components over the past decade. However, most earthquake damages were observed to the nonstructural components during and after the earthquakes. The primary objective of this research was to develop the seismic fragility of the piping system incorporating the nonlinear Tee-joint finite element model in the full scale piping configuration installed in critical facilities. The procedure for evaluating fragility curves corresponding to the first damage state was considered the effects of the top floor acceleration sensitivities for 5, 10, 15, and 20 story linear RC and steel building systems subjected to 22 selected ground motions as a function of ground motion uncertainties. The result of this study revealed that the conditional probability of failure of the piping system on the top floor in critical facilities did not increase with increased level of story height and in fact, story level in buildings can tune the fragilities between the building and the piping system.