A fuel cell system including: a fuel cell group; a refrigerant distribution passage; a pre-distribution refrigerant flow rate acquiring unit configured to acquire a first outlet temperature flow rate; a first outlet temperature detecting unit that is configured to detect a first outlet temperature; a voltage acquiring unit configured to acquire at least a first voltage that is a voltage of the first fuel cell; a current acquiring unit configured to acquire at least a first current; and a controller that calculates a first individual supply flow rate of the first fuel cell on the basis of the first voltage, the first current, and the first outlet temperature, and calculates a second individual supply flow rate of at least one second fuel cell other than the first fuel cell on the basis of the first individual supply flow rate and the pre-distribution refrigerant flow rate.