Selective decomposition by plasma generated in the aqueous phase was investigated as a means to remove ammonia accumulated as a byproduct in hydrazine hydrate (HH) fuel solution in a HH fuel cell system. When plasma was generated in an aqueous solution of ammonia, volatile ammonia molecules readily entered the plasma phase and were directly decomposed to form molecular hydrogen and nitrogen. On the other hand, non-volatile HH molecules in water were degraded by the secondary reaction with reactive oxygen species (ROS) such as hydrogen peroxide generated from the plasma decomposition of water. Because ammonia can preferentially enter the plasma and consume ROS via a redox reaction, HH decomposition is expected to be depressed. The present method was found to be a promising elemental technology in the practical usage of a HH fuel cell system.