A method for controlling a startup of a fuel cell system is provided. The method includes comparing a voltage generated in a fuel cell stack when hydrogen is supplied to a fuel electrode of the fuel cell stack for a set period of time with a first reference voltage. A voltage of a unit cell of the fuel cell stack is compared with a second reference voltage for load connection when the voltage generated in the fuel cell stack is higher than the first reference voltage. A load is connected to the fuel cell stack when the voltage of the unit cell of the fuel cell stack is higher than the second reference voltage for load connection.