A fuel cell system includes: a fuel cell stack that is formed of a plurality of serially connected fuel-cell cells that use fuel, gas and oxidant gas to generate electric power, a detecting unit that detects an output power generated by each of a first fuel-cell cell group and a second fuel-cell cell group that are grouped on the basis of a power generation performance factor; and an operating condition changing unit that changes an operating condition of the fuel-cell cells on the basis of a rate of deviation between the generated output power of the first fuel-cell cell group, detected by the detecting unit, and the generated output power of the second fuel-cell cell group, detected by the detecting unit.