A fuel cell system includes a first ion exchanger, a first fuel cell stack and a second fuel cell stack, a first temperature acquisition part and a second temperature acquisition part, a first power generation time acquisition part and a second power generation time acquisition part, a supply path, an ion concentration estimation part that estimates ion concentration of a refrigerant on the basis of the ion concentration estimated by the ion concentration estimation part, a determination part that determines an exchange timing of the first ion exchanger on the basis of the ion concentration estimated by the ion concentration estimation part, and a control part, and a first refrigerant flow path and a second refrigerant flow path are provided in series or in parallel.