A fuel cell system includes a fuel cell, a hydrogen tank, a hydrogen supply passage connecting the hydrogen tank and the fuel cell, a cutoff valve configured to cut off circulation of hydrogen in the hydrogen supply passage, a detection unit configured to detect a start of filling of the hydrogen tank with hydrogen, and a purge controller configured to close the cutoff valve in a case where the fuel cell system is stopped and the detection unit detects the start of filling with hydrogen in a state in which purge processing of purging the in-cell hydrogen flow passage is to be executed, and to execute processing of purging the in-cell hydrogen flow passage by causing hydrogen remaining on a downstream side of the cutoff valve in a hydrogen flow in the hydrogen supply passage to flow in the in-cell hydrogen flow passage as the purge processing.