In the present study, we report that the selection of operation mode is important to take the full advantage of nanofibrous membrane in enzyme immobilization. Silk fibroin nanofibrous membrane has been prepared by electrospinning, and a-chymotrypsin was immobilized as a model enzyme. When the immobilized enzyme was operated in the membrane reactor mode, the Michaelis constant, Km, was lower and the Vmax was higher compared to the batch reactor mode. No concentration gradient was observed in the membrane reactor mode and the immobilized enzyme was stable even after 7 times of re-use. Our results suggests that the enzyme immobilized nanofibrous membrane should be operated in the membrane reactor mode rather than in the bath reactor mode.