There are several ancient stone masonry structures of great archeological significance in earthquake- prone areas around the world. Kaʻba-ye Zartošt (Cube of Zoroaster) is a 14.0 m square in shape tower, which was built using white limestone blocks and dry joints. The tower dates back to the Achaemenid empire era and is located in the earthquake-prone area of Nagsh-e Rustam in Fars, Iran. Although, after approximately 2,500 years the tower is still standing, it is now in a severely deteriorated condition and may be vulnerable against future large in magnitude earthquakes. This paper presents the application of a previously developed three-dimensional numerical model based on the discrete element method of analysis to investigate the seismic behavior of the Cube of Zoroaster tower. The tower was represented by a series of distinct blocks separated by zero-thickness interfaces. The developed model allows finite displacements and rotations of distinct blocks while new contacts between the blocks are automatically recognized and updated as the calculation progresses. A series of non-linear dynamic analysis have been performed. To this end, the behavior of the tower to different ground shaking motions is discussed and the possible failure modes for each case are explored.