The removal efficiency of 22 selected trace organic contaminants by sequential application of granular activated carbon (GAC) and simultaneous application of powdered activated carbon (PAC) with membrane bioreactor (MBR) was compared in this study. Both sequential application of GAC following MBR treatment (MBR–GAC) and simultaneous application of PAC within MBR (PAC–MBR) achieved improved removal (over 95%) of seven hydrophilic and biologically persistent compounds, which were less efficiently removed by MBR-only treatment (negligible to 70%). However, gradual breakthrough of these compounds occurred over an extended operation period. Charged compounds, particularly, fenoprop and diclofenac, demonstrated the fastest breakthrough (complete and 50–70%, in MBR–GAC and PAC–MBR, respectively). Based on a simple comparison from the long-term performance stability and activated carbon usage points of view, PAC–MBR appears to be a better option than MBR–GAC treatment.