This study presents an application of performance-based assessment to establish fragility functions and evaluate the seismic reliability of an ancient stone pagoda in Korea. The pagoda was constructed of stone elements which were stacked over each other in layers without bonding material. To account for the discrete nature of this kind of structural configuration, the distinct element method is used to perform the incremental dynamic analysis to develop fragility functions. Three performance levels are specified on the capacity curve which is established based on non-linear pushover analysis. The randomness in seismic demand generation was considered when exciting the pagoda by a set of 23 input ground motion records, which were scaled into different intensity levels. The seismic response of the pagoda under different ground motions at several peak ground acceleration levels shows that the predominant frequency of the excitation is closely related to the behavior of this kind of structure. Ground motions with lower predominant frequency values induce stronger distortion to the pagoda than the ones with higher predominant frequency. The fragility functions estimated by maximum likelihood method show that earthquakes with peak ground motion of 0.469 g have a 50% probability of causing a collapse on the pagoda in the most conservative assessment. The probability of the pagoda collapsing within 50 years is 1.65% for the most earthquake-vulnerable site among the sites considered in the study.