This study was conducted to develop a method for analyzing protofagopyrins and fagopyrins in buckwheat extract by ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry multiple reaction monitoring (UPLC-MS/MS MRM), to validate the developed method, and to determine the conversion of protofagopyrins to fagopyrins by various light sources. Protofagopyrin E (PFE), protofagopyrin F (PFF), fagopyrin E (FE), and fagopyrin F (FF) were analyzed in Tartary buckwheat flower (TBF) extract, and PFE and PFF were identified for the first time. The linearity, limit of detection, limit of quantification, and precision were evaluated using the FF-rich fraction that was separated from the TBF extract. TBF contained the most PFF and FF among buckwheat plant parts and products. The contents of protofagopyrins and fagopyrins changed minimally in the TBF extract when it was not exposed to light. When the TBF extract was exposed to light, the contents of PFE and PFF decreased, and those of FE and FF increased. Blue (450 nm) and fluorescent (400−700 nm) lights more rapidly converted protofagopyrins to fagopyrins than the other lights.