A system for activating a fuel cell includes a flow meter for measuring the amount of water discharged from an outlet of the air electrode and an outlet of the fuel electrode; a pressure sensor for measuring the pressure at the respective outlets; and a back pressure regulator receiving flow values measured by the flow meters and pressure values measured by the pressure sensors, which are fed back from a controller, and regulating a pressure difference (ΔP=PCathode−PAnode) to be a value greater than 0. With the system, the activation time of a fuel cell and the amount of hydrogen used for the activation can be reduced, thus improving the productivity and manufacturing cost.