A microhole electrical discharge machining (EDM) system with adaptive fuzzy logic control and precision piezoelectric stage is developed in this study. A high-speed EDM monitoring system is implemented to measure the gap voltage, current, and ignition delay time, which are used to derive three input parameters—the average gap voltage, deviation in spark ratio, and change in the deviation in spark ratio—for the fuzzy logic control. Servo displacement and speed of the piezoelectric stage during each sampling duration are synthesized in real time by the adaptive fuzzy logic controller. Effects of the single and multiple input parameters, ignition delay threshold value, and maximum servo displacement and speed on the EDM drilling process are experimentally studied. Experimental results show that the fuzzy logic EDM control system yields a much more stable and efficient microhole EDM drilling process.