Disclosed is a fuel cell system and a method for controlling the fuel cell system. In the method, an external air temperature and a fuel cell temperature are monitored. When a vehicle having the fuel cell system mounted therein is keyed on, a shut-off duration of the fuel cell system, a maximum external air temperature for the shut-off duration and a maximum fuel cell temperature for the shut-off duration are calculated. A gas composition of a fuel cell at a key-on time is estimated using the shut-off duration, the maximum external air temperature and the maximum fuel cell temperature. An ignition condition of the fuel cell system is set based on the estimated gas composition. Ignition of the fuel cell system is performed based on the set ignition condition.