Some of the more than 350 Scutellaria species, such as S. baicalensis and S. lateriflora, have been used in traditional medicine and today play an important role in official phytotherapy. Other species have been less investigated, and their therapeutic potential is unknown. This is one of the few studies on Scutellaria brevibracteata subsp. subvelutina, and the first research of this species’ in vitro cultures. The aim of this study was to establish an in vitro culture and analyse its phytochemical profile and biological activity. In the methanolic extracts from biomass cultured on six solid Murashige and Skoog (MS) medium variants supplemented with different combinations of 6-benzylaminopurine (BAP) and 1-naphthaleneacetic acid (NAA) in the range 0.5–3 mg/L analysed by HPLC, the presence of specific flavonoids (baicalein, baicalin, wogonin, wogonoside, scutellarin, chrysin), phenylpropanoid glycosides (verbascoside, isoverbascoside), and phenolic acids (p-hydroxybenzoic, caffeic, ferulic, m-coumaric acids) was confirmed. The dominant metabolites were wogonoside and verbascoside with the highest content of 346 and 457 mg/100 g DW, respectively. Thus, the extract with the highest content of bioactive metabolites was selected for further research and subjected to evaluation of antioxidant and antimicrobial potential. The extract exhibited good free radical scavenging activity (IC50 = 0.92 ± 0.01 mg/mL) and moderate reducing power and chelating activity. The brine shrimp lethality bioassay proved its lack of biotoxicity. Antimicrobial activity was tested against sixteen strains of Gram-positive and Gram-negative bacteria and fungi. The strongest growth inhibitory activity was observed against Trichophyton tonsurans.