A fuel cell system includes a plurality of fuel cell stacks, an anode pipeline, a cathode pipeline, an anode discharge valve, a cathode supply valve, a cathode discharge valve, an anode pressure sensor, a cathode pressure sensor, and a control device. The control device determines whether a cross leak that is permeation abnormality of fuel gas or oxidant gas between an anode and a cathode on the basis of a pressure difference, which is difference between a pressure of the fuel gas and a pressure of the oxidant gas detected by the anode pressure sensor and the cathode pressure sensor in a stopped state of electric power generation of the plurality of fuel cell stacks, or a change in the pressure difference.