In this study, the long-term operational performance of building-integrated photovoltaic (BIPV) systems was analyzed in the Carbon Zero Building of the National Institute of Environmental Research (NIER) of South Korea, with a total area of 2449 m2. Three types of BIPV modules (glass to glass, glass to Tedlar/crystal, and amorphous) were installed in the building envelopes (roofs, walls, windows, atrium, and pergola) with a total capacity of 116.2 kWp. Over a five-year period, the average annual energy production was 855.6 kWh/kWp, the system loss ranged from 0.14 to 0.31 h/d, and the capture loss ranged from 0.21 to 1.81 h/d. The causes of capture losses were degradation of the power generation efficiency of the horizontal installation module due to the accumulation of dust and reduced energy production due to application of the same inverter for the crystal system module and amorphous module. As a result, the BIPV systems with an installation angle of 30° exhibited approximately 57% higher energy production than vertically (90°) installed systems under the same solar radiation. Moreover, horizontal (0°) BIPV systems exhibited up to 14% higher energy production than vertical BIPV systems.