A fuel cell electric power generation system includes an electric power generation subsystem, a fuel processing subsystem including a furnace, an oxidant subsystem, a water circulation subsystem, and a temperature control subsystem. Interactions between the subsystems are simplified and component integration improves thermal and electrical efficiency of the system. In one embodiment, a reformer, a fuel stream humidifier and a heat exchanger are disposed within the furnace, with the humidifier outlet fluidly connected to the reformer inlet and the heat exchanger outlet fluidly connected to a desulfurizer located outside of the furnace. The fuel processing subsystem can also include a shift reactor that exchanges heat with a cathode exhaust stream directed to the shift reactor from the power generation subsystem. After passing through the shift reactor, the cathode exhaust stream is preferably directed to the furnace burner.