The purpose of this study was to investigate the fermentation characteristics of Yakju using fresh sprouts from common buckwheat, a Daisan cultivar, and a tartary buckwheat Daikwan 3-3 cultivar to develop a functional Yakju, which is a traditional Korean liquor. As fermentation time increased, alcohol concentration and total sugar content (expressed as Brix degrees) increased, whereas reducing sugar content decreased. In particular, alcohol formation capability was maximized from the fourth to the seventh days of the second mashing stage during the fermentation procedure, which corresponded to the abrupt rise in mashing body temperature. The pH increased slightly when the titratable acidity was kept from increasing as fermentation proceeded. Quercetin and rutin were not present in the control group but their presence in Yakju with added buckwheat sprouts continuously increased with an increase in the fermentation period. Quercetin and rutin contents were higher in the Yakju with added Daikwan3-3 buckwheat sprouts than Yakju with added Daisan buckwheat sprouts. In conclusion, adding buckwheat sprouts improved Yakju quality during fermentation. Particularly, Yakju with added Daikwan3-3 buckwheat sprouts had superior fermentation characteristics and quality.