There is provided a technique to suppress water from remaining in a fuel cell and auxiliary machines after a stop of operation of a fuel cell system. A fuel cell system 100 includes a controller 10, a fuel cell 20, a cathode gas supply discharge system 30 and an anode gas supply discharge circulation system 50. The controller 10 serves as a termination process controller 15 to control a termination process that is performed when operation of the fuel cell 20 is to be stopped. In the termination process, the termination process controller 15 performs a quick warm-up operation to quickly increase the temperature of the fuel cell 20, subsequently performs a standard warm-up operation that has a lower temperature rise rate of the fuel cell 20 than that in the quick warm-up operation, and then performs a purging process to purge the fuel cell 20.