A method and apparatus for controlling a screen in an electronic device are provided. The method includes displaying a pop-up window in a display area, disposed over another application displayed in the display area. If a movement of the pop-up window is detected, and a portion of the pop-up window reaches a predefined area of the display area, the pop-up window is removed from the display portion. A selectable icon is displayed allowing a user to redisplay the pop-up window or alter an operational state of the pop-up window.