A fuel processor having a movable burner, a method of operating the fuel processor, and a fuel cell system having the fuel processor. The fuel processor includes a combustion chamber, a reformer burner, a portion of which is partially disposed inside the combustion chamber, a reformer which is heated by heat transfer from the combustion chamber, and a burner-moving apparatus that moves the reformer burner with respect to the combustion chamber. The method of operating the fuel processor includes determining the load on and a plurality of temperatures within the fuel processor and moving the reformer burner depending upon such information.