The object of the present invention is to provide a fuel cell system enabling an improvement in fuel consumption and a method for controlling thereof. A fuel cell system 1 includes a fuel cell 10, an air pump 21, an air supply channel, a hydrogen supply channel, a hydrogen tank, a hydrogen discharge channel, a hydrogen reflux channel, an air discharge channel, a purge valve 441, and a control device 30. The control device 30 includes a dilution judgment portion 31 judging whether dilution of hydrogen gas has been completed; an air increase portion 33 for increasing an air mass in the air discharge channel; a power production calculation portion 34 calculating an amount of power production based on the air mass increased; and a fuel cell drive portion 35 driving the fuel cell 10 to produce electric power to obtain the amount of power production calculated.