Flaxseed (Linum usitatissimum L.) is an important food, oil, and fiber crop of the family Linaceae. Although flaxseed has been consumed as a food ingredient for several centuries, its nutritional benefits have not yet been completely established. Flaxseed is a good source of lignans, nonstarch polysaccharides, and high-quality proteins. Hence, in this study, we aimed to prepare a bioactive kefir containing flaxseed and to examine the physicochemical characteristics of kefir containing different concentrations of flaxseed. We investigated the pH, and sensory evaluation of bioactive Kefir containing different concentrations of flaxseed. We investigated the pH, total anthocyanins (TAs), and sensory evaluation of bioactive Kefir containing different concentrations of flaxseed. The pH of this bioactive kefir decreased, whereas the TA content increased with increasing incubation time; however, these parameters were not affected by the amount of added flaxseed. As the addition rate of flaxseed increased, the scores for overall acceptability, texture, color, flavor, and taste in sensory evaluations were generally the same as or lower than the control. There were no significant differences in overall acceptability, texture, color, flavor, and taste between the control and treated groups. Therefore, further studies are needed to develop methods for production of health-improving kefir as a dietary supplement based on the functional properties of flaxseed.