Buckwheat possesses significant nutritional content and contains different bioactive compounds, such as total flavonoids, which enhance its appeal to consumers. This study employed single-factor experiments and the response surface methodology to identify the optimal germination conditions for enhancing the total flavonoid content in buckwheat sprouts through ultraviolet-B treatment. The research showed that buckwheat sprouts germinated for 3 days at a temperature of 28.7 °C while being exposed to ultraviolet-B radiation at an intensity of 30.0 μmol·m−2·s−1 for 7.6 h per day during the germination period resulted in the highest total flavonoid content of 1872.84 μg/g fresh weight. Under these specified conditions, ultraviolet-B treatment significantly elevated the activity and gene expression levels of enzymes related to the phenylpropanoid metabolic pathway, including phenylalanine ammonia-lyase, cinnamic acid 4-hydroxylase, 4-coumarate coenzyme A ligase, and chalcone isomerase. Ultraviolet-B treatment caused oxidative damage to buckwheat sprouts and inhibited their growth, but ultraviolet-B treatment also enhanced the activity of key enzymes in the antioxidant system, such as catalase, peroxidase, superoxide dismutase, and ascorbate peroxidase. This research provided a technical reference and theoretical support for enhancing the isoflavone content in buckwheat sprouts through ultraviolet-B treatment.