A fuel cell system comprises: a turbo type oxidizing agent pump, the rotary shaft of which is pivotally supported by an air bearing to take in and supply an oxidizing agent gas to a fuel cell by the rotary motion; an actual flow rate detection means for the oxidizing agent gas; a pressure adjustment means for the oxidizing agent gas; a rotary speed monitoring means for the oxidizing agent pump; and a control means which, when the rotary speed of the oxidizing agent pump is within the range of the minimum rotary speed that allows the rotary shaft to be pivotally supported by the air bearing, if the actual flow rate of the oxidizing agent gas is larger than a target flow rate, increases the pressure of the oxidizing agent gas via the pressure adjustment means.