Following the earthquake that shook the city of Gyeongju, Korea, in 2016, it became apparent that research on the safety of cultural heritages against the seismic hazards is necessary in Korea. Predictions of how historically significant stone pagodas would behave the earthquakes anticipated in near future, which are the subject of this study, is also required. In this study, the dynamic characteristics of 15 cultural heritage designated stone pagodas of Korea were investigated, including natural frequency and damping ratio, and the stiffness of the stone material and its contact area were determined using eigenvalue analysis by assuming the stone pagodas to be multi-degree-of-freedom structures. The results of this study enable the structural modeling of stone pagodas using a finite element analysis program and the method is expected to be useful in assessing the structural safety of stone pagodas against vertical loads as well as lateral forces, including earthquakes. Also, by identifying the dynamic characteristics of the structures, the results of this study can be utilized as a nondestructive testing method to determine the rigidity of cultural heritage structures and to identify inherent problems. The natural frequencies of the Korean stone pagodas were measured to be within 3.5~8.3㎐, excluding cases with distinct natural frequency results, and it was determined that the natural frequencies of the stone pagodas are influenced by various parameters including the height and joint stiffness of the structures.