Phased-mission system is a system whose mission consists of a sequence of non-overlapping phases described by different models. The focus of this paper is to apply the proxelbased simulation method to performability analysis of phasedmission systems. Phased-mission systems have been researched for a long time and they encompass a large number of systems in industry. Most of the existing methods impose some limitations on the systems they can analyze or face loss of accuracy. The proxel-based method allows for a general class of phased-mission systems to be analyzed without imposing the typical limitations on the models or sacrificing accuracy. Lower level components of systems can be described using any formalism, i.e. Petri nets or state-transition diagrams. We provide modification of the original algorithm of the proxelbased method, adapted to be applied to phased-mission systems. In addition, we present results from experiments performed using the presented approach.