A stone arch bridge is one of the excellent heritages in the civil engineering. In order to maintain and to evaluate the seismic response of these bridges, this paper proposes a numerical analysis tool by using the finite element method as a discrete deformation analysis incorporated with the friction-contact analysis. We call this method “Discrete Finite Element Model” in this paper, and we implement this numerical analysis with commercial FE software “LS-DYNA”. The realistic FE meshes are generated, and material properties are acquired by material testing. Finally, efficiency and applicability of the 3-Dimensional FE model are demonstrated with numerical results for a static loading test and a dynamic response with one of the observed seismic waves at Kumamoto earthquake 2016.