In this study, we optimized conditions for extraction of eleutherosides B and E from stem powder of Acanthopanax. To enhance eleutheroside B and E yields, Acanthopanax sessiliflorus Seeman and Eleutherococcus senticosus Maxim were pre-incubated with the following enzymes: Celluclast, Viscozyme L, Lactozyme, Lecitase, and Novozyme 33095. Treatment with Novozyme 33095, a commercial pectinase, for 3 h resulted in the highest yields of eleutherosides B and E from A. sessiliflorus and E. senticosus. Compared with extraction at 121°C for 120 min, at 121°C for 15 min after Novozyme 33095 pre-incubation increased eleutheroside B and E yields from A. sessiliflorus by 7% and 17%, respectively. In the case of E. senticosus, eleutheroside B and E yields increased by 25% and 29%, respectively.