Ammonium-containing wastewater could cause the promotion of eutrophication and a hindrance to the disinfection of water supplies. In this study, the feasibility of removing low-concentration ammonium nitrogen from synthetic and real wastewater by electrochemical oxidation was investigated. Using laboratory-scale electrochemical systems, the effects of chloride concentration, current density, anode materials, cathode materials, electrode gap, initial ammonium concentration and three-dimensional particles on the removal of ammonium nitrogen and current efficiency (CE) were evaluated. Ammonium nitrogen removal was mainly dependent upon anode materials and current density. The performance of two- and three-dimensional electrochemical oxidation systems was comparatively discussed. Both particle electrodes could enhance ammonium nitrogen removal and increase CE. However, the mechanism of the process seemed to be different. Moreover, the interaction of zeolites adsorption and electrochemical oxidation on the anode in a three-dimensional system could favor the regeneration of zeolites. Surface morphology of the used Ru-Ir-Sn/Ti anode revealed its longer working life of electrocatalysis. The result of ammonium degradation for a real wastewater treatment plant effluent showed the degradation rates in a three-dimensional system increased by 1.4 times those in a two-dimensional system.