A method and a system for controlling startup of a fuel cell are provided. The method includes sensing a startup request signal and boosting a Bi-directional high-voltage DC/DC Converter (BHDC) of a main bus stage when the startup request signal has been sensed by a controller. A valve of an air/hydrogen line is then opened together with the boosting of the BHDC and the startup of the fuel cell is completed by allowing an output of the fuel cell after the valve of the air/hydrogen line is opened.