A fuel cell system a includes a cooling water temperature raising unit that raises the temperature of a fuel cell stack by passing discharge gas of a process burner or hydrogen gas of a fuel processing unit and cooling water that is heated by the discharge gas of the process burner through flow paths formed on opposing surfaces of cooling separators formed of a metal and installed between a plurality of cells in the stack. Thus in the fuel cell system, when the temperature of the stack needs to be rapidly raised, for example, during a start up operation of the fuel cell system, the temperature of the stack can be rapidly raised using discharge gas at a high temperature or combustion heat of hydrogen gas, and heated cooling water, and thereby, significantly reducing the time required for the fuel cell system to be in regular operation.