A high gradient magnetic separation system for medical protein using affinity magnetic nano-beads has been developed. Medical protein such as monoclonal antibody or immunoglobulin is an important substance as a medicine for cancer etc. However; the separation system of these medical protein has very low separation rate and the cost of product is extremely high. The developed system shows very high separation efficiency and can achieve low cost by large production rate compared to the system now using in this field. The system consists of a 3T superconducting magnet cooled by a cryo-cooler, a filter made of fine magnetic metal wires of about 30μm diameter and a demagnetization circuit and a liquid circulation pump for solvent containing medical protein. Affinity magnetic nano-beads is covered with the medical protein after agitation of solvent containing the protein and nano-beads, then the solvent flows through the system and the beads are trapped in the filters by high gradient magnetic field. The beads are released and flow out of the system by the AC demagnetization of the filters using LC resonance circuits after discharge of the magnet. The test results shows 97.8% of the magnetic nano-beads in pure water were captured and 94.1% of total beads were collected.