This study investigates the influence of surface roughness on the performance of polymer electrolyte membrane fuel cells (PEMFCs) through computational simulations using COMSOL Multiphysics. Two distinct gas flow channel (GFC) models of serpentine and parallel GFC structures were analysed, featuring various surface roughness levels to examine their impact on gas pressure and velocity dynamics. Rough surfaces are modeled using trigonometric functions to replicate machining-induced variations. Finite element simulations were conducted, assessing the time-dependent relationship between gas pressure and velocity while considering different electrode phase potentials as a function of surface roughness. Rough surfaces generally enhance mass transport, water management, and current distribution compared to smooth surfaces. The results indicated that a surface roughness of approximately 1 µm optimizes PEMFC performance by balancing pressure and velocity, enhancing electrochemical reactions, and reducing excessive pressure drops within the cell. Notably, the 0.7 V operating voltage was found to be the most efficient, achieving rapid stabilization of pressure and velocity levels swiftly. The findings underscore the importance of precise control over GFC roughness to enhance PEMFC performance gains in commercial applications, especially when multiple cells are stacked to achieve high power outputs.