Provided is a method of controlling a pointer, such as changing between a pointer mode for activating the pointer and a search key mode for deactivating the pointer, in a mobile terminal having a pointing device. The method of controlling a pointer includes detecting movement input by the pointing device; identifying whether the detected movement satisfies a condition of changing a display mode; if the detected movement satisfies a condition of changing a display mode, displaying the pointer by changing the current display mode to a pointer mode; identifying whether a specific key is input; and if the specific key is input, hiding the pointer by changing the current display mode to a search key mode. Additionally, if elapsed time measured after displaying the pointer exceeds a predetermined value, the display mode of the mobile terminal may automatically be changed to a search key mode.