Membrane is one of the most important components in proton exchange membrane fuel cells (PEMFCs), which determines the transport phenomena, performance, and durability. With the rapid development of novel membranes, many transport coefficients in membranes applied in numerical studies are outdated due to the lack of experimental data for new membranes. In this review, the fundamentals of commercially available membranes are scrutinized, followed by the fundamental working mechanisms. A detailed examination of the transport phenomena within the membranes, including transport mechanisms, mathematical description, and experimental methods, is conducted for protonic conduction, electro-osmosis drag, diffusion, hydraulic permeation, and gas crossover, which are urgently needed for theoretical and numerical studies. It is found that various empirical or analytical correlations have been established to predict the transport coefficients of the membranes. However, empirical models may not be accurate for all types of membranes since there is no sufficient experimental data for a solid correlation and validation. The experimental methods reviewed in the present study can be applied for new membranes, which is essential to quantify the transport phenomena and its further impact on cell performance and durability. The key transport-phenomena-related factors that affect the performance and failure modes of membranes are also reviewed in this study, which helps to develop strategies in improving membranes’ performance and durability during operation. This review deepens the understanding of the short-term and long-term performance of the membrane in PEMFCs and provides important insights into the further design of novel membranes. •Scrutinized fundamental concepts and recent progress in membranes of PEMFCs.•Reviewed the transport phenomena in membranes of PEMFCs.•Summarized the transport coefficients and experimental methods for membranes.•Evaluated the effect of transport-phenomena-related factors on membrane performance.•Reviewed the effect of transport-phenomena-related factors on membrane durability.