Amorphous alloy (AA) is a high-performance metal material generally with significantly excellent mechanical and corrosion resistance properties and thus is considered as a desirable material selection for micro-scale articles. However, the microfabrication of AA still faces a variety of technical challenges mainly because the materials are too hard to process and easily lose their original properties, although at moderately high temperatures. In this study, jet-electrolyte electrochemical machining (Jet-ECM) was proposed to microfabricate the Zr-based AA because it is a low-temperature material-removal process based on the anode dissolution mechanism. The electrochemical dissolution characteristics and material removal mechanism of AA were investigated, and then the optimal process parameters were achieved based on the evaluation of the surface morphologies, surface roughness, geometrical profile, and machining accuracy of the machined micro-dimples. Finally, the feasibility was further studied by using Jet-ECM to fabricate arrayed micro-dimples using the optimized parameters. It was found that Jet-ECM can successfully microfabricate mirror-like surface AA arrayed precision micro-dimples with significantly high dimensional accuracy and geometrical consistency. Jet-ECM is a promisingly advantageous microfabrication process for the hard-to-machine AA.