Tungsten cemented carbide (WC-Co) is a widely applied material in micro-hole drilling, such as in suction nozzles, injection nozzles, and wire drawing dies, owing to its high wear resistance and hardness. Since the development of wire-electro-discharge grinding (WEDG) technology, the micro-electrical discharge machining (micro-EDM) has been excellent in the process of fabricating micro-holes in WC-Co material. Even though high-quality micro-holes can be drilled by micro-EDM, it is still limited in large-scale production, due to the electrode tool wear caused during the process. In addition, the high cost of precision micro-EDM is also a limitation for WC-Co micro-hole drilling. This study aimed to develop a low-cost desktop micro-EDM system for fabricating micro-holes in tungsten cemented carbide materials. Taking advantage of commercial micro tools in a desktop micro-EDM system, it is possible to reach half the amount of large-scale production of micro-holes. Meanwhile, it is difficult to drill the deep and high aspect ratio micro-holes using conventional micro-EDM, therefore, a cut-side micro-tool shaped for micro-EDM system drilling was exploited in this study. The results show that micro-holes with a diameter of 0.07 mm and thickness of 1.0 mm could be drilled completely by cut-side micro-tools. The roundness of the holes were approximately 0.001 mm and the aspect ratio was close to 15.