The effectiveness of hypochlorite cleaning for fouling mitigation of a prototype chlorine-resistant nanofiltration (NF) membrane was assessed for direct filtration of a secondary treated effluent. The chlorine resistance and separation performance of the prototype NF membrane were also compared to commercial NF and reverse osmosis membranes. The prototype chlorine resistant NF membrane did not show any changes in permeability and conductivity rejection after exposing a NaOCl solution for up to 5 × 10 4 ppm-h. By contrast, a considerable deterioration in rejection was observed for the other two commercial membranes. Direct filtration of a secondary treated effluent by the prototype NF membrane resulted in a progressive permeability reduction by up to 25% after 10 h of filtration. The membrane permeability was fully restored by hypochlorite cleaning with a 2000 ppm NaOCl solution for 1 h. Effective permeability recovery by hypochlorite cleaning was demonstrated with multiple hypochlorite cleaning cycles. Membrane fouling and hypochlorite cleaning were also simulated using solutions containing a model foulant (sodium alginate, humic acids or bovine serum albumin). Among them, an insufficient permeability recovery was observed for membrane fouling caused by humic acids. Further research is recommended to develop an improved hypochlorite cleaning protocol to control various membrane fouling.