A fuel cell system capable of adequately controlling the water content of a fuel cell is provided. An impedance reference value is stored in a memory for an impedance comparator. The impedance reference value is a reference value that is set in order to prevent the water content in a fuel cell from decreasing too much. The impedance comparator compares a measured impedance value supplied from an impedance operation unit with the impedance reference value and performs scavenging control based on the comparison result.