The treatment of reject water containing concentrated ammonia and non-biodegradable organics is a challenging task in wastewater treatment plants. To address this problem, we propose a novel process consisting of a selective ammonium-exchange resin and an ammonia electrooxidation reaction (AmER-AOR). Because an alkaline condition is essential for direct ammonia oxidation, the use of a bipolar membrane (BPM) was helpful. Nonetheless, an initial pH of 13 and KOH addition were required to maintain a high alkalinity for the complete elimination of ammonia. The linear sweep voltammogram elucidated the high pH requirement and ammonia oxidation promotion. When the current density varied from 30 to 80 mA cm−2, 60 mA cm−2 showed the highest current efficiency (30.39%) and the lowest specific energy demand (95.3 kWh/kg-N), indicating the most energy-effective condition. Increasing the initial concentration of ammonia from 0.1 M to 0.5 M improved the current efficiency (51.57%), demonstrating an additional energy-effective strategy for the AmER-AOR. The energy efficiency of pure H2 production in the cathodic chamber was 30%. To estimate the viability for practical applications, reject water collected from a local wastewater treatment plant was applied in the AmER-AOR. Notably, no significant difference in the ammonia removal rate was observed with synthetic wastewater. To the best of our knowledge, this is the first study that employs a BPM as a separator and OH− supplier for direct ammonia oxidation. Our findings reveal that the AmER-AOR with a BPM has promising practical applicability in the treatment of reject water and energy production.