Various ionic liquid-based aqueous two-phase systems (IL-ATPS) were evaluated to extract puerarin. The results indicated that the nature of ILs, the salting-out ability of salt, and the acidity and basicity of the salt-rich solution had important influence on the extraction efficiency. Various factors were optimized systematically, that is, the amount of IL, salt, puerarin, and short-chain alcohol. Under the optimal experimental conditions (the amount of K2HPO4 0.30-0.42 g/mL, [Bmim]Br 0.30-0.36 g/mL and 1.0 mL puerarin stock solution), the extraction efficiency of puerarin was over 99% by a single-step extraction, which indicated that the evaluated IL-ATPS was a prospective extraction medium. Finally, the IL-ATPS was successfully used to extract puerarin from Radix Puerariae Lobatae extracts.