In an apparatus and a method for controlling operation of a compressor, by removing deviation generated by resistance and inductance and removing an error in a stroke estimation value of a compressor, operation of the compressor can be accurately controlled. The apparatus includes a counter electromotive force detector for detecting a counter electromotive force generated at a motor of a compressor. A stroke calculator calculates a stroke estimation value of the compressor on the basis of the counter electromotive force, and a stroke controller controls a stroke of the compressor by varying a voltage applied to the motor on the basis of the calculated stroke estimation value and a stroke reference value.