Rhus verniciflua Stokes (RVS) is a widely used herbal plant with various biological properties. Our previous study using cultured neuronal cells showed that an ethanol extract of RVS had strong antioxidant properties. In this study, we characterized the antioxidant activity of the RVS ethanol extract and identified the active compounds responsible for this activity. From the RVS ethanol extract, we derived three water-eluted fractions and another three fractions eluted by organic solvents, and determined that the water-eluted fractions are what protect against reactive oxygen species (ROS) generated by iron and enzymes. Water-eluted fraction F(2) was the most efficient antioxidant. Moreover, DNA fragmentation and terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) staining experiments revealed that F(2) also protects against thymocyte apoptosis mediated by hydroxyl radicals. Finally, EI-MS, (1)H-NMR, and (13)C-NMR spectra signals confirmed that the fraction contained flavonoid derivatives, including fustin, quercetin, butein, and sulfuretin. These results suggest that the flavonoid derivatives in F(2) are the compounds in the RVS ethanol extract that act as antioxidants.