In this study, we sought to increase the anti-inflammatory activity of Scutellaria baicalensis extracts using a nanoencapsulation process. The ethanol extract of Scutellaria baicalensis was encapsulated with lecithin and two other extracts as follows: aqueous extraction at 100 °C for 24 h (AE), 70% ethanol extracts at 80°C for 24 h (EE), which were also compared as controls. The ethanol extract of S. baicalensis with lecithin was estimated to be 94.3 nm while the encapsulation efficiency of the nanoparticles was measured as 61.4% higher than other encapsulation processes. Antioxidant activity was also observed as 60% inhibition of DPPH radical scavenging activity, and nitric oxide production by RAW264.7 cells was also reduced by 5.1 μM after the addition of 0.5 mg/mL nanoparticles. Only 743.7 pg/mL of PGE2 was produced by RAW 264.7 macrophages after the addition of 0.5 mg/mL of nanoparticles, as compared to 1105.6 pg/mL and 962.3 pg/mL of PGE2 production after the addition of 1.0 mg/mL of aqueous and ethanol extracts, respectively. This is the first report, to our knowledge, of real-time penetration of nanoparticles into human fibroblasts using a confocal scanning microscope.