A compact autothermal (partial oxidation and steam reforming) fuel reactor is provided for implementation with a fuel cell system. The reactor includes a premixing chamber for premixing a volume of air, steam and fuel into an effluent, a thermal POX reactor, a first stage reforming segment, a post-premix chamber, and a second stage reforming segment. Further provided are a water/fuel vaporizer for supplying steam and fuel as a gas to the premix chamber and an airflow cavity disposed about the reactor for pre-heating air supplied to the premix chamber. The thermal POX segment operates during an initial start-up period for pre-heating the other components of the reactor. Once the other components achieve an operation temperature, the first and second stage reforming segments catalytically reform the effluent. The premix and post-premix chambers enable variance in the O/C and S/C ratios to be achieved as the effluent is reformed through the multiple stages.