Soybean sprouts are among the healthiest foods consumed in most Asian countries. Their nutritional content, especially bioactive compounds, may change according to the conditions of germination. The purpose of this study was to test the effect of chitooligosaccharide with different molecular weight and dosage on nutritional quality and enzymatic and antioxidant activities of soybean sprouts. The chitooligosaccharide elicitor strongly stimulated the accumulation of vitamin C, total phenolics, and total flavonoid. The stimulation effect was correlated with the molecular weight and concentration of chitooligosaccharide. With treatment of 0.01% of 1 kDa chitooligosaccharide, the nine phenolic constituents and six isoflavone compounds were significantly increased. The antioxidant capacity (DPPH radical and hydroxyl radical scavenging activity) and antioxidase activities (catalase and peroxidase) of soybean sprouts were also enhanced after treatment with chitooligosaccharide. The degree of chitooligosaccharide-induced elicitor activity increased as the molecular weight of chitooligosaccharide decreased. These results suggest that soaking soybean seeds in a solution of chitooligosaccharide, especially in 0.01% of 1 kDa chitooligosaccharide, may effectively improve the nutritional value and physiological function of soybean sprouts.