Micro-drills are widely used in the micro-hole machining of printed circuit boards. Helical flutes, the core feature of micro-drills, play a crucial role in chip discharge. Precision grinding technology is commonly used for machining the helical flutes in micro-drills. Grinding is a contact machining technology that generates a grinding force during the process. When the diameter of the micro-drill is minimal (Φ ≤ 100 µm), the grinding force is extremely prone to cause deformation or even fracture of the micro-drill, leading to a decreased yield. To overcome the above problem, the paper proposed an approach to fabricate a helical flute structure on the surface of a micro-drill by micro electrical discharge machining (micro-EDM) using a beryllium-copper-tin composite disc foil electrode (CDFE). Micro-EDM, a type of non-contact machining, can effectively avoid the disadvantage of grinding the helical flute of the micro-drill. Through an orthogonal experiment, the effects of the rotation velocity of the CDFE, machining voltage, and pulse duration ratio on the machining quality of the helical flutes were analysed in detail. Finally, with 4000 r/min CDFE rotation velocity, 24 V machining voltage, 1 µs pulse duration and 3 µs pulse interval, a helical flute structure with a surface roughness Ra of 0.381 µm was successfully machined on the surface of a 70 µm diameter micro-drill.