In this study, a numerical study was conducted on the flow characteristics of a cyclone separator for the disposal of medical waste. To analyze the composition of medical waste, samples were collected from medical facilities. Then, particle size analysis was conducted after the shredding process. A performance evaluation of the cyclone separator when collecting fine particles generated from five types of medical waste was also conducted. The flow characteristics generated inside the cyclone separator were analyzed, and the maximum tangential and axial velocities were 11.3 and 6.5 m/s, respectively. Depending on the diaper, ringer string, syringe, gauze, and cotton particles, more than 90% could be collected from particles sized over 148.2, 148, 25.3, 29.2, and 34.8 μm, respectively.