In a startup method for fuel cell systems, and more particularly, a startup method which makes the fuel cell systems rapidly reach a steady state operation by significantly decreasing the time taken to increase the temperature of the shift reactor catalyst, gas discharged from a burner that heats a reformer is supplied into the shift reactor. In the startup method of the fuel cell system, the fuel cell systems rapidly reach a steady state operation thereby significantly improving the utility of the fuel cell system. In addition, the fuel cell system is economical in that gases discharged from burners included in the fuel cell system and waste heat are used.