Over the years, building integrated photovoltaic system has been considered as a practical and climate conscious approach for building design, development and comfortable living. This paper investigates the mismatch in energy yields of PV system that is connected to grid situated over a building in Northern India for viability purposes. The system under consideration is of 330 kWp capacity; it consists of a large number of subarrays and experimental measurements were carried out of two subarrays (units) of identically rated components to explore the disparity between rated energy output at Standard Test Condition (STC) and the energy actually produced by the system as well as variations in electrical energy output between the units. It is found that the monthly mean energy differences between the subarrays is 75 kWh whereas the minimum and maximum energy differences are 12 kWh and 180 kWh respectively. These results show that there is notable decrease in energy output due to mismatch in system subarrays. The root cause mechanism causing the mismatch between the electrical energy output of two units is also discussed.