An object is to provide a technique of enhancing the accuracy of estimation of the water content of a fuel cell on the occurrence of localized drying of an electrolyte membrane. In a fuel cell system, until satisfaction of a second condition indicating that localized drying of the electrolyte membrane is eliminated after satisfaction of a first condition indicating that localized drying of the electrolyte membrane occurs, a water content estimator performs a second water content estimation process that estimates the water content of the fuel cell based on an output current value of the fuel cell, in place of a first water content estimation process that estimates the water content of the fuel cell based on an impedance of the fuel cell. The first condition is that an oxidizing gas stoichiometric ratio is equal to or higher than a predetermined reference value and that a first elapsed time has elapsed since the oxidizing gas stoichiometric ratio becomes equal to or higher than the predetermined reference value. The second condition is that an accumulated current value by accumulation of the output current value for a second elapsed time since satisfaction of the first condition is equal to or greater than a reference value of accumulated current value or that the oxidizing gas stoichiometric ratio is lower than the predetermined reference value and that a third elapsed time has elapsed since the oxidizing gas stoichiometric ratio becomes lower than the predetermined reference value.