Bioaugmentation with genetically engineered microorganisms (GEMs) in a membrane bioreactor (MBR) for enhanced removal of recalcitrant pollutants was explored. An atrazine-degrading genetically engineered microorganism (GEM) with green fluorescent protein was inoculated into an MBR and the effects of such a bioaugmentation strategy on atrazine removal were investigated. The results show that atrazine removal was improved greatly in the bioaugmented MBR compared with a control system. After a start-up period of 6 days, average 94.7% of atrazine was removed in bioaugmented MBR when atrazine concentration of influent was 14.5 mg/L. The volumetric removal rates increased linearly followed by atrazine loading increase and the maximum was 65.5 mg/(L·d). No negative effects were found on COD removal although carbon oxidation activity of bioaugmented sludge was lower than that of common sludge. After inoculation, adsorption to sludge flocs was favorable for GEM survival. The GEM population size initially decreased shortly and then was kept constant at about 10–10 CFU/mL. Predation of micro-organisms played an important role in the decay of the GEM population. GEM leakage from MBR was less than 10 CFU/mL initially and was then undetectable. In contrast, in a conventionally activated sludge bioreactor (CAS), sludge bulking occurred possibly due to atrazine exposure, resulting in bioaugmentation failure and serious GEM leakage. So MBR was superior to CAS in atrazine bioaugmentation treatment using GEM.