This study was conducted to provide a technical solution to treat effectively perchlorate from inorganic wastewater of zinc smelting. Despite an inhibition dissolved inorganic substances in the wastewater discharged from zinc smelting has demonstrated with the activity of microbes, biological treatment technology could reduce perchlorate to a satisfactory level under such stressful conditions. It was found that either conductivity or SO42- concentration of the wastewater was able to be used as the adequate index and the values were 2,450 μS/cm and 1,200 ppm respectively. When SO42- increased from 0 to 16,000 ppm (conductivity : 428 → 24,800 μS/cm), perchlorate biodegradation rate was reduced due to 1/10 times from 0.0365 to 0.0033 /h, however, most of perchlorate was removed under the condition of hydraulic retention time (HRT) at 0.5day and mixed liquor volatile suspended solid (MLVSS) at 2,000~3,000 ppm.