Seed germination with selenium (Se) is promising for producing Se-biofortified foods. Mungbean (Vigna radiata (L.) Wilczek) sprout is freshly eaten as a salad dressed with sauce, making it superior for Se biofortification. Since the Se safety range for the human body is extremely narrow, it is imperative to evaluate the genotypic responses of mungbean sprouts to Se. This study evaluated the Se enrichment capacity and interaction with flavonoids and antioxidant systems in sprouts of 20 mungbean germplasms. Selenium treatment was done by immersing mungbean seeds in 20 μM sodium selenite solution for 8 h. Afterward, the biomass, Se amounts, flavonoid (particularly vitexin and isovitexin) contents, antioxidant capacity, and key biosynthetic gene expressions were measured. Sprout Se content was 2.0-7.0 μg g −1 DW among the 20 mungbean germplasms. Selenium treatment differentially affected the biomass, total flavonoid, vitexin, isovitexin, antioxidant enzyme activities, and antioxidant capacities of the mungbean germplasms. Eight germplasms showed increased biomass (p < 0.05), the highest increasing by 127%, but 13 did not phenotypically respond to Se treatment. Seven and six germplasms showed varied levels of vitexin and isovitexin increment after Se treatment, the highest measuring 2.67-and 2.87-folds for vitexin and isovitexin, respectively. Two mungbean flavonoid biosynthesis genes, chalcone synthase (VrCHS) and chalcone isomerase (VrCHI) were significantly up-regulated in the germplasms with increased vitexin and isovitexin levels (p < 0.05). Moreover, Se enrichment capacity was significantly correlated with the vitexin, isovitexin, and antioxidant capacities. In conclusion, mungbean sprouts could be a useful Se-biofortified food, but the Se enrichment capacity and nutritional response must be determined for each germplasm before commercialization.