The aim of the study was to investigate the effects of microwave-assisted extraction (MAE) conditions (microwave power, extraction time, and ethanol concentration) on the efficiency of the extraction of phenolic compounds from selected plant species belonging to the genusScutellaria(i.e.,Scutellaria baicalensisandScutellaria lateriflora). The extracts from selectedScutellariaspecies were examined to establish the total phenolic content and the in vitro antioxidant and anti-inflammatory activity. The antioxidant capacity was determined by the ferric reducing antioxidant power (FRAP) and 2,2,1-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity methods. The anti-inflammatory activity was evaluated through the lipoxygenase (LOX) inhibitory assay. The phenolic profile of the extracts was characterized using ultra-high performance liquid chromatography coupled with diode array detection and high-resolution electrospray ionization mass spectrometry (UHPLC–DAD/ESI–HRMS/MS). Depending on the type of solvent and the extraction conditions used, the extracts obtained from selectedScutellariaspecies showed different total and individual phenolic content, as well as different antioxidant and anti-inflammatory properties. The results showed that allScutellariaextracts had high total phenolic content and exhibited strong ferric ion reducing power and free radical scavenging capacity and a significant ability to inhibit the LOX activity. In general, the 70% ethanol extracts contained more phenolic compounds, mainly flavones, flavanones, and their derivatives, and showed greater in vitro biological activity than other extracts. The highest levels of phenolic compounds and the strongest antioxidant and anti-inflammatory potential were found in extracts from the roots ofS. baicalensis. Optimal extraction conditions for all the plant materials tested were determined as the microwave power of 63 W, extraction time of 10 min, and 70% ethanol as the solvent.