A method of operating a light emitting diode (LED) display device is provided. The method includes determining idle time periods respectively corresponding to LED driving clock signals, based on a number of LED driving clock signals corresponding to one frame, controlling generation of the LED driving clock signals, based on the determined idle time periods, and driving an LED module in a unit of an LED line, based on the generated LED driving clock signals. As the LED display device automatically adjusts idle time periods of the LED driving clock signals, the occurrence of flicker in the LED display device may be reduced.