The present invention provides a method for removing residual water in a fuel cell, which controls the humidity of purge gases to effectively remove residual water in the fuel cell and to maintain the humidity in a membrane at a constant level, thus ensuring the durability of the membrane.For this purpose, the present invention provides a method for removing residual water in a fuel cell, characterized in that the relative humidities of purge gases supplied to an anode and a cathode are controlled to selectively reduce water content in the fuel cell and water content in a membrane.