We investigated the operating conditions of a baffled membrane bioreactor (B-MBR) under which long-term stable operation can be achieved through a continuous operation of a pilot-scale B-MBR. Under appropriate operating conditions, the B-MBR was capable of achieving sufficient treated water quality in terms of biochemical oxygen demand and concentration of total nitrogen. Excellent removal of total phosphorus was also achieved. In addition, the development of membrane fouling was in an acceptable level, indicating that stable continuous operation of B-MBR is possible under the operating conditions adopted in the present study. Estimation of the specific energy consumption in hypothetical full-scale B-MBRs operated under the conditions recommended from the findings obtained in the continuous operation of the pilot-scale B-MBR was also performed in this study. The results of estimation of energy consumption suggest that energy consumption in full-scale B-MBRs operated under the operating conditions mentioned above were in the range of 0.20–0.22 kWh/m3. The results obtained in this study strongly suggest that energy consumption in MBR operation can be significantly reduced by applying the concept of B-MBR.