A method for operating a fuel cell system including a fuel cell stack composed of a plurality of cells connected in series. The method includes the steps of: (a) supplying a fuel and an oxidant to anodes and cathodes of the cells, respectively, depending on a load to generate power at a constant voltage under constant voltage control; (b) temporarily suspending the supply of the oxidant with the fuel being supplied; and (c) lowering the constant voltage to a predetermined voltage simultaneously with or immediately before the suspension of the supply of the oxidant. According to this operation method, when the supply of the oxidant is suspended, a platinum catalyst in the cathodes can be reduced and reactivated in all the cells.