A fuel cell system includes: a fuel cell which generates electricity by supplying hydrogen to an anode electrode, and a reaction gas to a cathode electrode, an anode gas supply device which supplies hydrogen to the anode electrode, and a cathode gas supply device which drives a compressor using electric power generated by the fuel cell, and supplies pressurized reaction gas to the cathode electrode. The fuel cell system further includes a target pressure setting device which sets a target value for cathode pressure of the fuel cell, a correction device which corrects the target value in accordance with atmospheric pressure, and a control device which controls the cathode pressure of the fuel cell to the corrected target value. Efficient electric power generation can be performed in accordance with the ambient environment.