Many studies and considerable international efforts have gone into reducing greenhouse gas emissions. This study was carried out to improve the efficiency of flat-plate photovoltaic thermal (PVT) systems, which use solar energy to produce heat and electricity simultaneously. An efficiency analysis was performed with various flow rates of water as the working fluid. The flow rate, which affects the performance of the PVT system, showed the highest efficiency at 3 L/min compared with 1, 2, and 4 L/min. Additionally, the effects of nanofluids (CuO/water, Al2O3/water) and water as working fluids on the efficiency of the PVT system were investigated. The results showed that the thermal and electrical efficiencies of the PVT system using CuO/water as a nanofluid were increased by 21.30% and 0.07% compared to the water-based system, respectively. However, the increase in electrical efficiency was not significant because this increase may be due to measurement errors. The PVT system using Al2O3/water as a nanofluid improved the thermal efficiency by 15.14%, but there was no difference in the electrical efficiency between water and Al2O3/water-based systems.