During the operation of vanadium redox flow battery, the vanadium ions diffuse across the membrane as a result of concentration gradients between the two half-cells in the stack, leading to self-discharge reactions in both half-cells that will release heat to the electrolyte and subsequently increase the electrolyte temperature. In order to avoid possible thermal precipitation in the electrolyte solution and prevent possible overheating of the cell components, the electrolyte temperature needs to be known. In this study, the effect of the self-discharge reactions was incorporated into a thermal model based on energy and mass balances, developed for the purpose of electrolyte temperature control. Simulations results have shown that the proposed model can be used to investigate the thermal effect of the self-discharge reactions on both continuous charge–discharge cycling and during standby periods, and can help optimize battery designs and fabrication for different applications.