Disclosed is an apparatus and method for controlling a reciprocating compressor capable of inexpensively and exactly controlling a position of a piston in a cylinder, by which a top clearance is minimized according to the information of a phase difference between a square wave of a piston stroke and a square wave of a current supplied to the compressor. The apparatus comprises a driving section for driving the reciprocating compressor by varying an angle or ignition in response to a control signal; a current phase detecting section for outputting a square wave corresponding to the detected current supplied to the compressor; a stroke phase detecting section for outputting a square wave corresponding to a stroke of the compressor; and a control section for controlling the angle of ignition of the driving section according to the phase difference between the square wave produced from the current phase detecting section and the square wave produced from the stroke phase detecting section.