A fuel processor system capable of circulating fuel processor system gases, e.g. reformate, anode exhaust, and/or combustor exhaust, through a fuel processor provides advantages. The system fuel cells discharge hydrogen-containing anode exhaust and oxygen-containing cathode exhaust, The fuel processor converts hydrogen-containing fuel to hydrogen-containing reformate to fuel the fuel cells. A catalytic combustor coupled with a vaporizer reactor is positioned in series downstream from the fuel cells. A bypass passage connects an outlet of at least one of the fuel processor, the fuel cells, the catalytic combustor, and the vaporizer reactor to the inlet of the fuel processor. The bypass passage is operable to circulate a fuel processor system gas to the inlet of the fuel processor.