This study investigated the microstructure and machining characteristics of a Zr38.5Ti16.5Cu15.25Ni9.75Be20 bulk metallic glass (Zr-BMG) alloy machined using electro-discharge machining (EDM). After EDM, the hardening effect near the outer surface of the electro-discharge machined (EDMed) Zr-BMG alloy originated from the surface carbides of the recast layer, ZrC and TiC. The thickness of the recast layer, crater size, and the surface roughness increased with greater pulse energy. Furthermore, the EDM can generate a porous recast layer and convert the Zr-BMG alloy surface into a carbide surface, which is a potential method to fabricate biomaterials. Experimental results also show that the material removal rate of this alloy in the EDM process was significantly related to the pulse current IP and pulse duration τP. Many electro-discharge craters and recast materials were observed on the surface of the EDMed Zr-BMG alloy. The surface roughness of the EDMed Zr-BMG alloy was found to obey the empirical equation of Ra = β(IP × τP)α.