A method for non-linear dynamic analysis of wall masonry structures is presented. The method takes advantage of a Generalized Matrix Formulation (GMF) for the serviceability and ultimate analysis of structures composed of arches and/or masonry walls, in which open and solid walls are described as equivalent frame systems. This formulation has been complemented with a cyclic constitutive model and an algorithm for the integration of the equation of motion, resulting in a numerically efficient method for non-linear analysis in time domain of complex masonry systems.