A fuel cell system includes first and second fuel cells, first and second coolers cooling coolant, first and second coolant supply path from the coolers to the fuel cells, first and second coolant discharge paths from the fuel cells to the coolers, a detour path connecting the first coolant supply path and the first coolant discharge path bypassing the first cooler, an adjusting device adjusting a flow rate of coolant of the detour path, first and second connection paths connecting the coolant supply paths and the coolant discharge paths, first and second opening/closing valves in the connection paths, and a controller configured to, when there is a possibility of flooding, suspend power generation of the first fuel cell and control the adjusting device or the first cooling device such that a temperature of the coolant of the first fuel cell increases, and open the opening/closing valves.