The work deals with the structural analysis of an historic masonry building, Palazzo del Capitano in Mantua, subject to significant static instabilities due to an overturning of the longitudinal facades, probably related to ground settlements. The exact geometry of the structure is acquired by means of the laser scanning technique and thanks to previous investigations, the main mechanical properties of the materials are reasonably well defined. Based on these information a three-dimensional finite element model of the entire structure is implemented, taking into consideration all the geometrical (contact between not connected panels and large displacement effects) and material (elasto plastic damage behavior of the masonry) nonlinearities, in order to investigate the seismic behavior of the structure by means of nonlinear dynamic analysis. The outcome of the analysis points out that the longitudinal facade, overlooking Piazza Sordello, is poorly constrained both to the floors and to the transverse bracing elements, therefore not able to counteract its deformation when a seismic event occurs. Finally suggestions to reduce the seismic vulnerability of the building are critically assessed by the implemented finite element model.