The hairy roots (HRs) of Scutellaria baicalensis are widely used and consumed worldwide as a medicine, especially in Asian countries, due to their biological and pharmacological activities. The HRs of this plant are rich in secondary metabolites. However, the optimal method and solvents for the extraction of secondary metabolites from S. baicalensis HRs have not been well studied. Therefore, in this study, S. baicalensis HRs were extracted with different solvents, including water (WE), 99.9% pure methanol (PM), 70% aqueous methanol (AM), 99.9% pure ethanol (PE), and 70% aqueous ethanol (AE). The phenolic and flavonoid compounds and various antioxidant activities of each extract were measured. The AE extract (16.85 ± 0.15%) had a higher yield, which led to the highest accumulation of total phenolic content (TPC) and total flavonoid content (TFC), and antioxidant activity. The TPC and TFC were highest in AE (66.03 ± 0.44 mg GAE/g and 40.11 ± 1.31 mg QE/g, respectively), whereas WE, PM, and PE showed lower values in all assays. In addition, the highest antioxidant activities, such as DPPH, ABTS, and SOD-like scavenging activities and reducing power, were achieved in the AE extract compared to the other solvent extracts. Based on these results, the AE extract showed the highest phenolic and flavonoid accumulation and antioxidant activities, highlighting its potential use in the manufacture of useful materials from S. baicalensis HRs and its novel applications.