In the treatment of disorders, bio-electrodes are used to be implanted into the patients’ deep brain for long-term stimulation. This paper presents a custom design and flexible fabrication process of bio-electrode for treating neural disorders using rapid prototyping (RP) technique. A 3D model of the bio-electrode is designed and the photosensitive resin electrode prototype is fabricated on the laser rapid prototyping machine, and then the bio-electrode is fabricated using this electrode prototype and the silicon rubber mold and winding technique. The spatial distribution of the electric field fabricated of the bio-electrode is analyzed, and the optical photomicrograph reveals that the cylindrical surfaces of the polyurethane of the bio-electrode have smooth surface and no visible microcracks, and the spiral lines are arranged densely and have no defects of loose and falling and partly protruding. The electrochemical experiments show that the electrochemical process of the bio-electrode is reversible and the bio-electrode has good functionality and stability property.