This work was aimed at the definition of a chromatographic method able to separate and quantify impurities present in sapropterin-containing drugs during an accelerated stability study. The chromatographic method was applied to the orphan drug Kuvan® and to its corresponding generic sapropterin Dipharma (Diterin®), both of which are approved for the treatment of hyperphenylalaninemia-induced symptoms. The two products tested had a similar manufacture date and both had an approved stability shelf-life of three years. Samples were analyzed by HPLC at T = 0 and after six months of storage at 40 °C and 75% relative humidity. Identification of the impurities was supported by a detailed mass spectrometry and MS/MS profile. The analysis demonstrated an overall higher stability for the Diterin® formulation, which was related to a lower increase of some impurities compared to Kuvan®.