Scutellaria L. is a diverse genus of the Lamiaceae (Labiatae) family of over 300 herbaceous plants commonly known as skullcaps. Various species of Scutellaria are used as ethnobotanical herbs for the treatment of ailments like cancer, jaundice, cirrhosis, anxiety, and nervous disorders. Scutellaria incana L., commonly known as the Hoary skullcap, is a traditional medicinal plant used by native Americans as a sedative for nervousness or anxiety. S. incana metabolites were identified by comparing their high-performance liquid chromatography (HPLC) retention times and mass spectra with those of the corresponding authentic standards. Where standards were unavailable, the structures were characterized on the basis of their tandem mass spectrometry (MS/MS) spectra following collision-induced dissociation (CID) and the accurate masses of the corresponding deprotonated molecules [M-H]− (mass accuracy ± 5 ppm). A total of 40 flavonoids, including two phenolic glycosides, were identified from leaves, stems, and roots of S. incana. Differences in the flavonoid composition between leaves, stems, and roots in S. incana were observed although the flavonoid profile of S. incana is consistent with other Scutellaria species. Further work should focus on assessing the potential of S. incana as a source of these bioactive metabolites.