A fuel cell system includes: a fuel cell that is supplied with a reaction gas to generate electricity; a plurality of auxiliary components used for power generation of the fuel cell; and a control device that causes the fuel cell to generate electricity when a predetermined scavenging start condition is satisfied and controls the auxiliary components using electric power generated by the fuel cell to perform a scavenging process of removing water in a flow path of the reaction gas using the reaction gas, during a stop period in which electric power is not supplied to a load from the fuel cell system.