A method and an apparatus are provided for performing a function corresponding to a recognized user input through a touch screen. The method includes displaying a window of an application; displaying a setting menu of the application; receiving a selection for at least one item in the setting menu; recognizing an input object that performed the selection; registering the input object as an object for executing a function corresponding to the at least one item selected by the input object; detecting an input by the input object in the application window; and executing the function in response to the input by the input object.