In this paper, the experiments were conducted for application of ammonia to fuel cell system. If ammonia is dissociated by heating on the suitable catalyst, it becomes 75% of hydrogen and 25% of nitrogen. The authors have proposed the new hydrogen generation system using ammonia for fuel cells and designed an ammonia dissociator and an ammonia distiller. The separator and the distiller for residual ammonia are necessary even in the optimal conditions obtained in the experiment. It could be demonstrated that the fuel cell system with the ammonia separator and the distiller. Then it can be possible to continuously operate fuel cells.