Electrochemical discharge machining (ECDM) is found to be a potential process for the microdrilling of glass wafers. However, some degree of heat-affected zone resulting from the thermal energy during ECDM produces several inherent problems that might be major issues, such as over cut and taper hole. To improve the quality of the ECDM microhole, a flat sidewall-flat front tool electrode is designed to reduce taper phenomena due to the sidewall discharge. In addition, a pulse voltage is applied to improve the heat-affected zone in the rectified dc voltage. The experimental results show that the combination of flat sidewall-flat front tool and pulse voltage conspicuously increases the machining accuracy while retaining the machining rate. This experimental investigation provides a new method that overcomes the disadvantages of conventional ECDM.