Electrochemical oxidation of ammonium ions (NH4+) by using a three-dimensional electrode (TDE) composed of IrO2–Ta2O5/Ti anode and bamboo carbon was carried out in this paper. Experimental results reveal that the NH4+ oxidation follows first-order kinetics at lower NH4+ concentration and the rate constant is highly dependent on the applied current density, dosage of chlorine ions and initial NH4+ concentration. In addition, increasing current density, more Cl− dosage and higher initial NH4+ concentration are beneficial for NH4+ removal. By inspecting the relation between rate constant and those operating factors, an overall empirical equation for estimation of the rate constant of NH4+ oxidation is presented. The estimated model is in good agreement with the experimental results and it could also be used for accurate design of the TDE system.