A fuel cell system includes a first fuel cell having first unit cells stacked together, a second fuel cell having second unit cells stacked together, a first voltage detector, a second voltage detector, and a controller. The first voltage detector detects voltage of the first unit cells for every “N” unit cells on average, and the second voltage detector detects voltage of the whole second fuel cell, or detects voltage of the second unit cells for every “M” unit cells on average. The controller determines whether any of the first unit cells is in a fuel deficiency state, by referring to a detection result of the first voltage detector, and performs a cancellation process to cancel the fuel deficiency state, on the first fuel cell that is in a power generating state, while stopping power generation of the second fuel cell, when an affirmative decision is obtained.