In this study, the effects of ZnO/water nanofluid and pure water as working fluids on the electrical and thermal energy efficiencies of a photovoltaic thermal system (PVT) are numerically investigated. The governing equations are discretized and solved using the pressure-based finite volume method by the ANSYS Fluent 16.2 software. The 3D numerical model is validated by comparing the simulation results with those of the measurements. The experiments are performed on selected days in August and September at the Ferdowsi University of Mashhad, Mashhad, Iran. To investigate the reliability of the measurements, an uncertainty analysis is performed for the experiments. The effects of the important operating parameters on the electrical and thermal energy efficiencies of the PVT system with ZnO/water nanofluid are studied. Moreover, the Taguchi method is applied to determine the optimum performance of the nanofluid based PVT system. The considered parameters include: absorbed solar irradiation, wind speed, ambient temperature, coolant inlet temperature, coolant mass flow rate, and nanoparticles mass fraction in the ZnO/water nanofluid. Based on the results of this study, reducing the coolant inlet temperature from 40 degrees C to 20 degrees C enhances the thermal energy efficiency of the nanofluid based PVT system by 16.21%. Moreover, it is found that the considered parameters in this study have slight effects on the electrical energy efficiency of the PVT system. The Taguchi analysis shows that the coolant inlet temperature is the most effective parameter on the efficiency of the nanofluid based PVT system.