In recent years, electrodialysis has been often considered as an appropriate method to treat industrial and/or municipal wastewater containing pharmaceutically active compounds. However, the scarcity of information on the ion transport mechanisms through the membranes, especially concerning occurrence of possible sorption phenomena, has limited the process implementation in practice. The present work aims to evaluate, by chronopotentiometry, the transport of sulfamethoxazole (SMX) through a cation- (CEM) and anion-exchange membrane (AEM) using synthetic solutions at different concentrations (0.001–0.1 g/L) and pH conditions (1.6 for CEM and 9 for AEM). The dominant mechanism of mass transfer under overlimiting current conditions at each membrane/solution system was determined. The potential drop profile measured during and after application of current pulses, as well as the transition times obtained from the curves, showed that sorption occurs at/in both membranes, especially for the AEM. Besides, this phenomenon was reversible for the CEM and irreversible for the AEM under the conditions evaluated herein. The chronopotentiograms of the AEM showed that the intense occurrence of water dissociation with the most diluted solution caused chemical equilibrium shifts in the membrane/electrolyte system, leading to formation of neutral SMX species that can impair the electrodialysis performance. The results obtained are useful for optimizing the electrodialytic treatment of SMX-containing solutions as well as of other compounds with similar physicochemical properties.