Water flooding remains a critical challenge that hinders the operation of fuel cells at high current and power densities. Here, we develop a novel gas diffusion layer (GDL) featuring quadrilaterally patterned perforations to boost the water drainage capability in proton exchange membrane fuel cells. When the perforations are vertically arranged to flow channels, the fuel cell can achieve a peak power density of 1.43 W cm–2 and a current density of as high as 5400 mA cm–2, far outperforming those with commercial GDLs with and without a microporous layer by 28.6% and 58.8%, respectively. Pore-scale simulations reveal that the patterned perforations reduce the breakthrough pressure and facilitate water removal, thus improving oxygen diffusion in the perforated GDLs, while cell-scale simulations show that the vertically arranged perforations to flow channels significantly enhance water removal to the adjacent channels due to the improved in-plane permeability, thereby reducing liquid water saturation and boosting cell performance.