The Energy Payback Time (EPBT) and Life-cycle Cost Analysis (LCCA) of a building integrated semi-transparent photovoltaic thermal (BiSPVT) system are carried out for different climatic and geographic zones. These two performance criteria are adversely affected by the shadow of the neighborhood’s buildings and obstacles. For countering the shadow effect, the BiSPVT system is proposed to install with optimum tilt and azimuth angle. The relative height, plan orientation, plan area, position, and horizontal distance of neighboring buildings are critical parameters in determining these angles to generate maximum energy. The proposed thermal model accurately calculates these angles and the output energy under various weather conditions at different places. The model assumes a water flow over the BIPV panel from an overhead tank, in view of increasing the efficiency of PV panel. The periodic nature of relevant parameters is considered in the thermal modeling of the BiSPVT system. The cost of energy produced by the proposed system ranges between 1.12 and 2.03 US$/ kWh depending on the climatic conditions of the place, and the EPBT of the system is found to be ranging between 11.6 years to 20.1 years which is lower than the expected service life (30 years) of the modules.