The present invention relates to a fuel cell system and a method for operating the same. The method of the present invention includes: igniting a fuel by an ignition element to generate flames to allow the fuel to carry out an exothermic combustion reaction in a burner, and introducing a reforming reaction material into an evaporator to vaporize the reforming reaction material; transmitting heat generated from the exothermic combustion reaction to a reactor, and introducing the vaporized reforming reaction material into the reactor to perform a reforming reaction and generate hydrogen gas; and introducing the hydrogen gas into a fuel cell stack member to generate electricity. Accordingly, the fuel cell system and the method for operating the same provided by the present invention can reduce start-up time and avoid the additional consumption of electricity.