Because electrode wear in microelectrical discharge machining significantly deteriorates the machining accuracy, the electrode wear must be compensated in process to improve the geometric accuracy of the product. Therefore, there has been a substantial amount of research on electrode wear and the compensation for EDM processes. In this study, a novel control method for a micro-EDM process using discharge pulse counting is proposed. The method is based on the proportional relationship between the removed workpiece volume and the number of discharge pulses. A model-based control was designed using the relationship between the pulse frequency and gap distance, and implemented in an actual micro-EDM system. Experimental results demonstrated that the developed method makes two- and three-dimensional micro-EDM milling processes fast and accurate without complex path planning to compensate electrode wear.