Scutellaria baicalensis root extracts have been useful for external skin care and have been commercialized for years. Here, a comprehensive study was conducted to investigate the difference between 20% propylene glycol (PG) and water used as the storage solvent for a time course analysis of their remaining biological activities and ingredient compositions versus their freshly prepared conditions. Of the four major components in the 20% PG solvent, more than 80% of the components were retained after storage for two months, but in water only baicalin and wogonin were retained. The relative antibacterial activities, antioxidant properties and anti-inflammatory activities of the 20% PG solvent group were better than those of the water solvent group. Taken together, we demonstrated that these activities improved when PG, a common solvent used in many product formulas, was used as the storage solvent for the S. baicalensis extract.