Nowadays, the application of renewable energies such as solar energy in the building sector has increased notably considering the adverse impacts of climate change on human life; hence many studies have focused on the application of photovoltaic panels in buildings. In the current study, a 3D computational fluid dynamics (CFD) model has been developed to evaluate the performance of a newly designed building-integrated photovoltaic (BIPV) system. Given the negative influence of overheating on the lifespan and performance of PV panels, their passive air cooling has been studied. Further, the potential of rooftop-mounted solar panels in passive ventilation of buildings by generating natural convective currents has been explored. The developed CFD model takes into consideration the effects of radiation, conduction, and buoyancy-driven natural convective currents generated by solar PV panels which are heated due to the exposure to solar radiation heat flux. The results suggest that applying a high surface emissivity for the part of the roof beneath the PV panels intensifies the natural convective currents which in turn provides better cooling for PV panels with higher cooling effects at higher solar heat fluxes. Up to a 34% increase in the convective mass flow rate and a 3 K decrease in the mean temperature of the panels were attained by modifying the emissivity of roof surface. Such a 3 K decrease in the operating temperature of the PV panels can enhance their efficiency and lifespan by about 1.56% and 21%, respectively. Based on the operating conditions and system characteristics, the BIPV system yielded an air change rate (ACH) in the range of 3–13 which was considered to be highly prevalent in providing the required passive ventilation for a wide range of applications. It was also observed that the flow dynamics inside the building were affected by both the amount of solar heat load incident on the solar panels and the emissivity of the roof surface behind the panels.