A fuel cell system includes a first fuel cell, second fuel cell, first voltage detector, second voltage detector, and controller. The first voltage detector detects voltage of first unit cells of the first fuel cell for every “N” unit cells on average, and the second voltage detector detects voltage of the second fuel cell as a whole, or detects voltage of second unit cells of the second fuel cell for every “M” unit cells on average, where “M” is larger than “N”. The controller determines whether any of the second unit cells is in a fuel deficiency state, based on the detection result of the first voltage detector, when a predetermined condition under which states of the first fuel cell and the second fuel cell are regarded as being close to each other is satisfied.