Puerarin is a C-glycoside of daidzein, one of the major bioactive ingredients isolated from the root of Pueraria lobata, which has a wide spectrum of pharmacological effects. Although puerarin is well-known for its effective antioxidant activity, there is seldom a systematic theoretical study on its radical scavenging activity. Herein, the free radical scavenging ability of puerarin was investigated systematically by density functional theory (DFT) calculations. The reaction activity was compared with daidzein as well. Three reaction pathways: hydrogen atom transfer (HAT), single electron transfer followed by proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET) were discussed and compared by thermodynamic parameters such as bond dissociation enthalpy (BDE), ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA), and electron transfer enthalpy (ETE). The reaction kinetics of puerarin with special radicals •OH and •OOH were also studied. The results obtained may be of great significance for better understanding the relationship between the antioxidant properties and structural design of puerarin, as well as other antioxidants.