A fuel cell system includes: a fuel cell; a voltage detector; a current detector; an alternating current signal supply unit; a phase difference calculation unit configured to calculate, based on detected alternating voltage and detected alternating current, a phase difference between the detected alternating current and the detected alternating voltage; and an estimation unit configured to estimate, in accordance with the phase difference, an electric power generation distribution feature amount representing an electric power generation distribution in a cell surface of the fuel cell, with use of a predetermined relationship between the electric power generation distribution feature amount and the phase difference. The electric power generation distribution feature amount includes a value indicating a difference between a maximum value and a minimum value of local current density in the cell surface.