We investigated the operating conditions of a baffled membrane bioreactor (B-MBR) under which long-term stable operation can be achieved through the continuous operation of a pilot-scale B-MBR. Under appropriate operating conditions, the B-MBR was capable of achieving excellent 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 degree of membrane fouling was acceptable, indicating that stable continuous operation of a 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 by the findings was also performed in this study. The results suggest that energy consumption in full-scale B-MBRs would be in the range of 0.20–0.22 kWh/m3. These results strongly suggest that energy consumption in MBR operation can be significantly reduced by applying the concept of a B-MBR.