Intensive membrane cleaning can be used with ceramic membranes since they are physically/chemically robust. It might therefore be possible for membrane bioreactors (MBRs) to be operated under the condition of a high membrane flux when ceramic membranes are used with such intensive membrane cleaning. In this study, bench-scale MBRs equipped with flat-sheet ceramic membranes were operated for long periods. Circulation of granular materials (cylindrical polyurethane) in the tank and frequent chemically enhanced backwash (CEB) were used as intensive physical cleaning and chemical cleaning in this study, respectively. Experiments were carried out with synthetic wastewater. The use of granular materials, which can cause significant damage to polymeric membranes (Kurita et al., 2015), was effective for controlling the formation of cake (deposition of microbial flocs) on the surface of the ceramic membranes. When both mechanical cleaning using the granular materials and CEB with 1000 ppm of sodium hypochlorite (NaClO) were applied, contrary to an expectation, evolution of reversible fouling (formation of a transparent gel layer on the membrane surface) became uncontrollable, whereas irreversible fouling was effectively controlled. The use of NaClO induced release of organic macromolecules via biomass decay, leading to the evolution of reversible fouling. When the intensity of CEB with NaClO was adequately lowered, with the aid of the mechanical cleaning using the granules, the bench-scale MBR could be operated stably under an elevated membrane flux for a long period (>70 days). It was postulated that the adjustment of CEB intensity preferably altered properties of organic macromolecules released from biomass: the structure of the gel layer was porous when the CEB intensity was lowered. When CEB is used in MBRs, it is thus important to balance cleaning efficiency and its harmful effect on biomass. When adequate CEB is used with intensive mechanical cleaning, MBRs with ceramic membranes can be operated under high flux conditions.