Despite pharmaceuticals being widely detected in water-bodies worldwide, what remain unclear are the effects of high pharmaceutical concentrations on the treatment efficiency of biological wastewater treatment processes, such as membrane bioreactor (MBR) systems. This study investigated the efficiency of MBR technology in the treatment of synthetic wastewater containing a mixture of five typical pharmaceuticals (ofloxacin, sulfamethoxazole, sulfamethylthiadiazole, carbamazepine and naproxen) with a total concentration of 500 µg/L. Both the control MBR (MBRc) without pharmaceutical dosing and the MBR operated with high influent pharmaceutical concentrations (MBRe) were operated under room temperature with the same hydraulic retention time of 11 h and the same sludge retention time of 30 d. The removal efficiency rates of total nitrogen and total phosphorus were 83.2% vs. 90.1% and 72.6% vs. 57.8% in the MBRc vs. MBRe systems, and both MBRs achieved >98% removal of organics for a 180-day period. The floc size decreased, and membrane fouling became more severe in the MBRe system. Microbial diversity increased in the MBRe system and the relative abundances of functional microbe differed between the two MBRs. Furthermore, the total relative abundances of genes involved in glycolysis, assimilating nitrate reduction and nitrification processes increased in the MBRe system, which could account for the higher organics and nitrogen removal performance. This work provides insights for MBR operation in wastewater treatment with high pharmaceutical concentrations.