Microcystis aeruginosa is one of the most commonly detected cyanobacteria in aquatic systems. Therefore, this study evaluated the removal efficiency of total (cell-bound and dissolved) microcystin (MC) by a hybrid process combining powdered activated carbon (PAC)-submerged hollow fiber membrane and compared the hybrid process performance with that of PAC adsorption and submerged hollow fiber membrane processes separately. The results indicated that up to 84% of the total MC was removed using the PAC adsorption stand-alone process, while 90% of it was removed by submerged hollow fiber membrane stand-alone process (with a 10 μg/L feed concentration). When the PAC dose of 20 mg/L and equilibrium time of 480 min were applied with a 51.9 μg/L feed concentration to the hybrid process, the removal efficiency of total MC increased to 99%. Moreover, the cell-bound and dissolved MC concentrations in the permeate were 0.34 and 0.65 mg/L, respectively. This permeate concentration level was ensured by the World Health Organization (WHO) as the guideline value for MC (1 mg/L). Overall, the hybrid process combining PAC-submerged hollow fiber membranes can be successfully used as an alternative advanced treatment technology to mitigate total (cell-bound and dissolved) MC.