This research numerically investigates a 3D sinusoidal-fined-based photovoltaic thermal system (FPVTS), which is of a high rate of productivity. The working fluids studied in this work are Cu/water nanofluid and pure water. Simulation accuracy has been verified against published literature data, which showed good agreement. Initially, three configurations including, a PV module, a simple channel photovoltaic thermal system (SPVTS), and the FPVTS, under the same base conditions, were numerically examined and compared. The results revealed that the proposed FPVT system has higher electrical and thermal exergy and energy performances in contrast with the two additional cases. The outcomes show that the FPVTS with Cu/water NF as the working fluid increased both overall exergetic and energetic efficiencies by 2.24% and 7.55%, respectively, compared with the SPVTS via pure water as the working fluid. In addition, a quasi-transient simulation for the FPVTS subject to daily weather conditions has been done. The maximum values for the overall exergy and energy efficiencies are 18.08% and 80.24%, which occurred at hours 12 and 9, respectively, for nanofluid. Also, the impact of miscellaneous quantities comprising volume fraction, volumetric flow rate, and coolant inflow temperature, on the FPVTS’s performance has been studied. Results indicate that high flow rates are more advantageous from an energy viewpoint, while low flow rates are more efficient from an exergy perspective. Low inflow temperatures increase energy efficiency while cutting exergy efficiency.