A system and method for controlling a fuel cell of a vehicle are provided. The method includes sensing a time point when pressure control is necessary by sensing whether an output of the fuel cell is additionally necessary or whether the fuel cell can be in a dry-out state. In response to sensing that the pressure control is necessary, a required valve opening degree of an air outlet is derived by substituting a target air pressure for a data map. A fuel cell air outlet valve is then adjusted based the derived valve opening degree of the air outlet.