The inevitable diffusion of vanadium ions across the membrane can cause considerable capacity loss and temperature increase in vanadium redox flow batteries (VRFBs) over long term operation. Reliable experimental data of the permeability rates of vanadium ions are needed for membrane selection and for use in mathematical models to predict long-term behavior. In this paper a number of ion exchange membranes were selected for detailed evaluation using a modified approach to obtain more accurate permeation rates of V2+, V3+, VO2+ and VO₂⁺ ions. Three commercial ion exchange membranes—FAP450, VB2 and F930—are investigated. The obtained diffusion coefficients are then employed in dynamic models to predict the thermal behavior under specific operating conditions. The simulation results prove that smaller and more balanced permeability rates of V2+ and VO₂⁺ ions are more important to avoid large temperature increases in the cell stack during stand-by periods at high states-of-charge with pumps off.