Seismic fragility functions for unreinforced masonry buildings were derived based on the incremental dynamic analysis of eight representative inelastic numerical models for application to Korea's earthquake damage estimation system. The effects of panel zones formed between piers and spandrels around openings were taken into account explicitly or implicitly regarding stiffness and inelastic deformation capacity. The site response of ground motion records measured at the rock site was used as input ground motion. Limit states were proposed based on the fraction of structural components that do not meet the required performance from the nonlinear static analysis of each model. In addition to the randomness of ground motion considered in the incremental dynamic analysis explicitly, supplementary standard deviation due to uncertainty that was not reflected in the fragility assessment procedure was added. The proposed seismic fragility functions were verified by applying them to the damage estimation of masonry buildings located around the epicenter of the 2017 Pohang earthquake and comparing the result with actual damage statistics.