A method of managing a gas turbine engine variable area fan nozzle includes the steps of operating a variable area fan nozzle according to a first operating schedule. An icing condition input is evaluated to determine the likelihood of ice presence. The first operating schedule is altered to provide a variable area fan nozzle position if ice is likely present or actually present to provide an icing operating schedule different than the first operating schedule. The first operating schedule corresponds to the flaps at least partially open at air speeds below a first airspeed. The altering step includes closing the flaps below the first airspeed as part of the icing operating schedule. The variable area fan nozzle position is adjusted according to the icing operating schedule. A fan is arranged in a fan nacelle that includes a flap configured to be movable between first and second positions. An actuator is operatively coupled to the flap.