The staged anaerobic fluidized membrane bioreactor (SAFMBR) is effective to remove organic substances with reduced sludge production by minimizing excess waste sludge. This study investigated the removals of four pharmaceuticals present at trace levels in municipal wastewater by using a SAFMBR. The target pharmaceuticals included ibuprofen, naproxen, carbamazepine, and diclofenac. A pilot-scale SAFMBR with hydraulic retention times (HRTs) from 4.5 to 13.5 hr was established and operated for 450 days with a municipal wastewater spiked with four pharmaceuticals. In the results, the BOD and COD removals were effective and limitedly affected the presence of pharmaceuticals. The BOD removal efficiencies in the anaerobic fluidized membrane bioreactor (AFBR) and anaerobic fluidized membrane bioreactor (AFMBR) were 63.5 ± 28.6% and 81.6 ± 25.1%, respectively. However, the treatment efficiencies of four pharmaceuticals varied. Naproxen that contains electron donating group was treated efficiently (63.8%∼72.1%), whereas the removal efficiencies of ibuprofen (25.0%∼32.4%), carbamazepine (16.6–18.5%), and diclofenac (non-detected) remained low. Ibuprofen was less efficient to compete with other electron acceptors in an anaerobic environment. For pharmaceuticals such as carbamazepine with a high acid dissociation constant (pKa = 13.9) or diclofenac with a high octanol-water partition coefficient (log K OW = 4.51), sorption onto the sludge could be one critical process affecting their concentrations in the water phase. By being positively charged at neutral pH and/or hydrophobic, the pharmaceuticals were initially adsorbed onto sludge, followed by being desorbed when sludge decayed after long operating hours. Nitrogen balance was analyzed to indicate the decay of the bacteria in the AFMBR. Increasing the HRTs only slightly improved the treatment efficiencies (e.g., the naproxen removal was increased from 63.8% to 72.1% when the HRT was increased from 4.5 to 7.5 h). The different processes responsible for the removals of these pharmaceuticals were more critical and their effects were limitedly changed by HRT adjustment, indicating the importance of knowing the properties of a pharmaceutical for selection of a proper treatment approach.