To alleviate water flooding in cathode electrodes of polymer electrolyte fuel cells (PEFCs), it is necessary to understand the water transport inside diffusion media and design the electrode/channel structure for facilitating the water discharge from porous electrodes to gas channels. The authors proposed the novel modified structure combining the electrode perforation with the channel hydrophilization in their previous study and revealed that its structure has the possibility of encouraging the through-plane water removal from the diffusion media and the oxygen diffusivity to the reaction sites. This study investigated the effects of perforation size and cell compression on the water transport in the cathode diffusion media of the structure-modified cell using x-ray radiography. The constant current operation tests were also conducted to characterize the cell performance. It was shown that the 300 µm perforation and low compression have a large effect on encouraging the in-plane water drainage from the diffusion media to the groove or hole, resulting in reducing the voltage loss due to the water flooding. This innovative structural modification can be put to practical use because of its simple manufacturing process and low cost.