Microwave-assisted extraction (MAE) is known as a more environmental-friendly process with economic advantages in terms of less time, less solvent, less energy and less waste than the current reflux method that is time-consuming. MAE was applied to extract three pesticides (quintozene, tolclofos-methyl and procymidone) from ginseng in a pesticide residue analysis and eliminate pesticide contaminants from ginseng prior to production of the ginseng extracts. The optimal conditions for pesticide extraction from ginseng were 50% in power (150 watts), 2 minutes, 20 mL hexane and 2.0 g sample. The results of optimal conditions were compared with those of Soxhlet method (7 hours, 150 mL hexane). The recoveries between two methods were almost same while time and amount of solvent used in MAE were significantly decreased in comparing with those in the Soxhlet methods. When the 45% ethyl alcohol as a extraction solvent was applied to eliminate pesticides from ginseng prior to the production of the ginseng extracts, it was found that 100% quintozene, 69% tolclofos-methyl and 83% procymidone were eliminated from ginseng. The data showed that MAE may be used to eliminate pesticide contaminants in ginseng prior to making the ginseng extracts.