A fuel cell system includes a fuel cell constructed by plural stacked cells, a circulation path through which a thermal medium is circulated into each cell, a heater for heating the thermal medium, a bypass path through which the thermal medium is circulated into a part of each cell while bypassing the other part thereof, and a flow control valve for controlling a flow amount of the thermal medium circulated in the bypass path. The thermal medium can be circulated into only the part of each cell in a warm-up operation, so that the part of each cell is collectively heated. An amount of the thermal medium circulated into the other part of each cell is controlled, so that all of each cell is finally warmed up in the warm-up operation.