Heat generation in electric double layer capacitors (EDLCs) may lead to temperature rise and reduce their lifetime and performance. This study aims to measure the time-dependent heat generation rate in individual carbon electrode of EDLCs under various charging conditions. First, the design, fabrication, and validation of an isothermal calorimeter are presented. The calorimeter consisted of two thermoelectric heat flux sensors connected to a data acquisition system, two identical and cold plates fed with a circulating coolant, and an electrochemical test section connected to a potentiostat/galvanostat system. The EDLC cells consisted of two identical activated carbon electrodes and a separator immersed in an electrolyte. Measurements were performed on three cells with different electrolytes under galvanostatic cycling for different current density and polarity. The measured time-averaged irreversible heat generation rate was in excellent agreement with predictions for Joule heating. The reversible heat generation rate in the positive electrode was exothermic during charging and endothermic during discharging. By contrast, the negative electrode featured both exothermic and endothermic heat generation during both charging and discharging. The results of this study can be used to validate existing thermal models, to develop thermal management strategies, and to gain insight into physicochemical phenomena taking place during operation.