Disclosed herein is a method of purging a fuel cell, by which water present in fuel cell stacks is discharged outside the fuel cell stacks together with gas by opening and closing a purge valve, including: conducting a short-period purge several times using the purge valve; and conducting a long-period purge once using the purge valve, wherein the short-period purge and the long-period purge are repeatedly conducted. The method of purging a fuel cell is advantageous in that the short-period purge is conducted several times using a purge valve and then the long-period purge is conducted once, and these short-period purges and the long-period purge are repeatedly conducted, so that the problems occurring when only a short-period purge or only a long-period purge is conducted can be solved, with the result that the efficiency and performance of the fuel cell are improved and the fuel cell can be stably operated.