The water content estimation apparatus for a fuel cell includes an estimating unit for estimating a residual water content distribution in a reactant gas flow channel and a moisture content distribution in an electrolyte membrane in a cell plane of a single cell while taking into consideration water transfer that occurs between an anode electrode and a cathode electrode via the electrolyte membrane between the anode electrode and the cathode electrode. The fuel cell system performs control based on an estimation result by the estimating unit so that the fuel cell assumes a predetermined water condition.