Proper thermal management of photovoltaic (PV) module can increase its efficiency. Among thermal active and passive techniques, phase change materials (PCMs) represent an effective thermal management route, thanks to their large latent heat at constant temperatures. In this paper, a phase change material integrated photovoltaic module with inclusion of heat sink is proposed to get lower and uniform distribution of temperature along the PV module. The PCM is selected according to the environmental conditions of a specific location. A comprehensive two-dimensional model of the proposed system is developed and analyzed in commercial COMSOL-Multiphysics software. The governing equations are solved numerically using finite element methods and simulations are carried out. Four different combinations are considered for the proposed system with small and large variations of PCM height and with and without including heat sink. The performance analysis is carried out for the climatic conditions of the Atacama Desert having high solar radiation and ambient temperature. The effect of the natural convection is also considered during the solid–liquid phase of the PCM. The effects of PCM height on the performance parameters of the proposed system are studied. The performance of four different cases of the proposed system is also compared. The findings of this study can be used to effectively design the cooling system for thermal management of photovoltaic modules installed in desert locations specifically.