The effects of exogenous methyl jasmonate (MeJA) on phytochemical production in buckwheat sprouts cultivated under dark conditions (0, 1, 3, 5, and 7 d) were investigated by metabolomic analysis, using ultra performance liquid chromatography-quadrupole-time-of-flight (UPLC-Q-TOF) mass spectroscopy (MS) and partial least-squares-discriminant analysis (PLS-DA). MeJA-treated and control groups showed no differences in growth but were clearly discriminated from each other on PLS-DA score plots. The metabolites contributing to the discrimination were assigned as chlorogenic acid, catechin, isoorientin, orientin, rutin, vitexin, and quercitrin, which have various health effects. Moreover, isoorientin, orientin, rutin, and vitexin were assigned as the main phytochemicals of sprouts cultivated under dark conditions. The accumulation of these metabolites caused the phenolic compound content and antioxidant activity of the sprouts to increase. Further, this study revealed that their accumulation resulted from the stimulation of the phenylpropanoid pathway by MeJA treatment. Therefore, these metabolites may be useful for better understanding the effects of MeJA on buckwheat sprout phytochemicals and contribute to improving the functional quality of the sprouts.