A fuel cell system (100) includes two supply passages (30, 32) for supplying the hydrogen to the anode (14). Valves (22, 23) which control flow amounts of the hydrogen passing through the two supply passages (30, 32) are provided. An exhaust passage (34) which outputs exhaust gas from the anode (14) is provided on the supply passage, and a valve (24) is also provided. When the valve (24) on the exhaust passage (34) is closed, the flow amount ratios of the hydrogen passing through the two supply passages (30, 32) are varied in time. Therefore, impurities such as nitrogen can be diffused. Thereby, a hydrogen purge amount can be reduced.