A building-integrated photovoltaic (BIPV) system integrates solar modules into the exterior structure of buildings. Particularly, in countries with limited land area and many high-rise buildings, such as Korea, BIPV is a favorable technology for securing building energy production capacity. Herein, a three-dimensional dynamic thermal analysis was conducted on the most widely applied curtain wall-integrated and spandrel-integrated BIPV systems in Korea. The analysis involved deriving the rear temperature of the module to examine the power-generation efficiency and output under actual operating conditions. The power generation efficiency of the curtain wall-integrated BIPV system decreased by a maximum of 4.35% compared with that of the individual modules, whereas it decreased by a maximum of 5.10% for the spandrel-integrated system.