The International Maritime Organization (IMO) ballast water management agreement (International Convention for the Control and Management of Ship's Ballast Water and Sediments) came into force on September 8, 2017. This study evaluated the disinfection performance of electrolysis, UV treatment, and electrolysis + UV combined, to improve the treatment of zooplankton (size ≥ 50 μm), which is expected to strengthen the standards for biodegradation efficiency. Among the methods used, the disinfection time leading to 100% death was in the order: electrolysis > electrolysis + UV > UV process. For the same level of disinfection performance, the amount of electricity required for the electrolysis, UV, and electrolysis + UV processes were 1,300 W.s, 8,400 W.S, and 4,500 W.s, respectively. The combination of electrolysis + UV process for inactivation of zooplankton in ballast water did not show a synergic effect owing to the slow disinfection time and high power consumption.