The effects of inhomogeneous compression of gas diffusion layers (GDLs) on local transport phenomena, within a polymer electrolyte membrane (PEM) fuel cell were studied theoretically. The inhomogeneous compression induced. by the rib/channel structure of the flow field plate causes partial deformation of the GDLs and significantly affects component parameters. The results suggest that inhomogeneous compression does not significantly affect the polarisation behaviour or gas-phase mass transport. However, the effect of inhomogeneous compression on the current density distribution is evident. Local current density under the channel was substantially smaller than that under the rib when inhomogeneous compression was taken into account, while the current density distribution was fairly uniform for the model which excluded the effect of inhomogeneous compression. This is caused by the changes in the selective current path, which is determined by the combination of conductivities of components and contact resistance between them. Despite the highly uneven current distribution and variation in material parametres as a function of GDL thickness, the temperature profile was relatively even over the active area for both the modelled cases, contrary to predictions in previous studies. However, an abnormally high current density significantly accelerates deterioration of the membrane and is critical in terms of cell durability. Therefore, fuel cells should be carefully designed to minimise the harmful effects of inhomogeneous compression.