A fuel cell purging method is provided to effectively prevent fuel cell deterioration and degradation of durability of the fuel cell by performing hydrogen purging at a point in time at which negative pressure of an anode peaks after a fuel cell vehicle is stopped. The fuel cell purging method includes stopping the driving of a fuel cell vehicle and continuously measuring pressure of an anode of a fuel cell after the fuel cell vehicle is stopped. Additionally, hydrogen is supplied to the anode when the measured pressure of the anode reaches a negative pressure peak time point.