A thermally integrated fuel cell system includes a stack zone, a burner zone and a low temperature zone. The fuel is combined with steam and passed sequentially through a primary reformer and a secondary reformer. Air is split into two parallel streams and preheated in a low temperature heat exchanger. One air stream passes to a high temperature heat exchanger while the other passes to a radiative heat exchanger. The air and fuel streams are equalized in an equalization heat exchanger before entering the fuel cell stacks. The stack exhaust is combusted in an afterburner. Afterburner exhaust heats the primary reformer, the high temperature heat exchanger, the low temperature heat exchanger and steam generator. The stack zone includes the stacks, the secondary reformer, the radiative heat exchanger and the equalization heat exchanger. The burner zone includes the afterburner, the primary reformer and the high temperature heat exchanger. The low temperature zone includes the low temperature heat exchanger and the steam generator.