Electrical discharge machining (EDM) is one of the most widespread nonconventional machining processes. Recently, a low-power micro-EDM process was introduced using a cylindrical electrode. Since its development, micro-EDM has been applied effectively to micromachining, and because the device setup for this process is simple, it is suitable for a microfactory that minimizes machines to fabricate small products economically in one system. In the EDM process, however, the electrode is also removed along with the workpiece. Therefore, the electrode shape and length vary as machining progresses. In this paper, a control method using a high speed realtime voltage measurement is proposed to regulate the rate and amount of material removed. The proposed method is based on the assumption that the volume of the workpiece removed in a single discharge pulses is nearly constant. The discharge pulses are monitored and controlled to regulate the amount of material removed. For this purpose, we developed an algorithm and apparatus for counting the number of discharge pulses. Electrode wear compensation using pulse number information was applied to EDM milling in a microfactory, in which a slight tilt of the workpiece may occur. The proposed control method improves the machining quality and efficiency by eliminating the inaccuracies caused by electrode wear and workpiece tilt.