A programmable impedance controller and a method of operating prevent or substantially reduce internal noise and an influence from external noise lasting for a long time. The programmable impedance controller for comparing a pad voltage of a pad connected to an external determination impedance with a reference voltage, and for outputting an impedance control signal, and for performing a digital coding to an impedance code corresponding to the impedance control signal, includes a clock controller and a counter. The clock controller outputs a first clock signal in a reset mode and outputs a second clock signal in an operating mode, in response to an applied clock signal. The counter sequentially updates code data, one code step per clock period, in response to the first clock signal in the reset mode, and outputs update code data. In an operating mode, the counter outputs the update code data updated in the reset mode in response to the second clock signal.