In order to understand the origins of performance variations in unitized regenerative fuel cells (URFCs), bifunctional catalyst layers (BCLs) fabricated with two different methods, i.e., ink deposition on membrane or GDL, were designed in this paper. The performances of the two different methods were evaluated, and their reaction dynamics were measured by electrochemical impedance spectra. The different BCLs, caused by the different preparation processes, were found to influence the fuel cell performance. The cell potentials of the URFCs using platinum sprayed onto the gas diffusion layer (GDL) are above 0.100V higher than those with platinum sprayed onto the membrane at 800mAcm−2 in fuel cell (FC) mode. The mass transport resistances of the URFCs at different operation modes were also compared. It was proved that the platinum layer formed by applying platinum onto the GDL could prevent the cell from water flooding in FC mode. However, it was found that the cell performance changed slightly in water electrolysis mode with different BCLs. The electron conduction path was also found to be hindered by an IrO2 agglomerate, which led to a decrease in cell performance. The highest and lowest round-trip efficiencies of the URFC with different BCLs were 42.1% and 22.3%, respectively, at 800mAcm−2.