A fuel cell system has a fuel cell stack and a controller. The fuel cell stack is formed by stacking cells. The controller executes first cell voltage recovery processing when the cell voltage of a first cell group, placed at each end of the fuel cell stack, is below a first lower limit voltage threshold and executes second cell voltage recovery processing, which is different from the first cell voltage recovery processing, when the cell voltage of a second cell group, placed at substantially the center of the fuel cell stack, is below a second lower limit voltage threshold.