In this paper, a comparison of overall performance of Building integrated semi-transparent photovoltaic thermal (BiSPVT) system with traditional rooftop semi-transparent photovoltaic system (RtSPV) in outdoor condition is experimentally investigated. The numbers of PV modules in RtSPV and BiSPVT are 32 and 96 respectively of 75Wp each. To make the comparison between the two systems, the PV array of BiSPVT system is divided into three equal sets. Hence, electrically one set of PV array of BiSPVT system is equal to whole PV array of RtSPV system. The electrical components of both systems such as photovoltaic (PV) modules, cross sectional area of wires used, solar power conditioning unit (PCU), batteries etc. are identical. The experimental results for the above mentioned systems were obtained at 24th September, 2017 which was one of the clear day during offset of monsoon season in Varanasi, India. From previous experiments, under normal operation it was found that the electrical performance of BiSPVT was less than that of RtSPV system. This was due to acquired thermal energy by thermal room which ultimately increases the PV cell temperature. So in the work, on BiSPVT system water is flown (mass flow rate is 1.81 kg/sec on PV array) to bring down the PV cell temperature and check its performance. Moreover, the comparison of performance is made through water flow on PV array of BiSPVT system for intermittent duration (i.e. 10th to 14th hour) and RtSPV system without any water flow. It is found that the electrical performance of BiSPVT system in comparison to RtSPV system is increased.