A Light Emitting Diode (LED) driver circuit and a Pulse Width Modulation (PWM) controlling circuit thereof is provided. The LED driver circuit includes a voltage detector connected to a plurality of LED arrays, the voltage detector being configured to determine a connection status of each of the LED arrays according to a level of a feedback voltage of each of the LED arrays, and detect a minimum feedback voltage from the feedback voltage of each of the LED arrays that are determined to be connected, a controller configured to output a control signal to control boosting of the LED arrays according to the detected minimum feedback voltage, a PWM signal generator configured to output a PWM signal corresponding to the outputted control signal, and a driving voltage generator configured to supply a driving voltage commonly to the LED arrays according to the PWM signal.