The effect of compression on the actual structure and transport properties of the carbon cloth gas diffusion layer (GDL) of a polymer electrolyte fuel cell (PEFC) are studied here. Structural features of GDL samples compressed in the 0.0–100.0 MPa range are encapsulated using polydimethylsiloxane (PDMS) and by employing X-ray micro-tomography to reconstruct direct digital 3D models. Pore size distribution (PSD) and porosity data are acquired directly from these models while permeability, degree of anisotropy and tortuosity are determined through lattice Boltzmann (LB) numerical modelling. The structural models reveal that structural change proceeds through a three-step process, while PSD data suggests a characteristic peak in the pore diameter of 10–14 μm and a decrease in the mean pore diameter from 33 to 12 μm over the range of tested pressures. A mathematical relationship between compression pressure and permeability is determined based on the Kozeny–Carman equation, revealing a one order of magnitude reduction in through-plane permeability for a two order of magnitude increase in pressure. The results also reveal that the degree of anisotropy peaks in the range of 0.3–10.0 MPa, suggesting that in-plane permeability can be maximised relative to through-plane permeability within a material-specific range of compression pressures.