A fuel cell system includes a heat-generation amount detection device for detecting a heat generation amount in a fuel cell, and an evaporation amount controller for controlling an evaporation amount of water in the fuel cell based on the detected heat generation amount. The heat generation amount is detected based on an output electric power of the fuel cell, an output current thereof or a temperature thereof. The evaporation amount of water in the fuel cell is controlled by adjusting at least one humidification amount of hydrogen and oxygen to be supplied to the fuel cell, or by adjusting at least one flow amount of hydrogen and oxygen to be supplied to the fuel cell.