A fuel cell system includes: a processing unit configured to perform an activation process of temporarily reducing a cathode potential of a single fuel cell to a target potential for a duration time at a processing frequency; a cationic impurity amount estimating unit configured to estimate an amount of cationic impurities included in an electrolyte membrane of the single fuel cell; and a process degree determining unit configured to determine, when the amount of cationic impurities is large, a degree of the activation process which is higher than that determined when the amount of cationic impurities is small by performing at least one action among actions of changing conditions of the activation process, the actions including an action of reducing the target potential, an action of increasing the duration time, and an action of increasing the processing frequency. The processing unit performs the activation process to the determined degree.