Pharmaceuticals and personal care products (PPCPs) are ubiquitous in wastewater streams, but little is known regarding their roles in membrane fouling during the operation of membrane bioreactors (MBRs). This study attempted to understand the role of ciprofloxacin exposure in control of filamentous bulking as well as membrane fouling mitigation. Compared with the control MBR, results show that the ciprofloxacin could selectively inhibit and kill filaments present in the mixed liquor, and, as a consequence, the sludge settleability improved significantly. The addition of ciprofloxacin had little influence on organic removals and nitrification, but had an adverse effect on denitrification. In addition, the sludge flocs exposure to ciprofloxacin still kept in compact structure; specifically, granular sludge was finally formed possibly due to the increase of polysaccharides in extracellular polymeric substances (EPS). Characterization by nuclear magnetic resonance (NMR) corroborated the enrichment of polysaccharides in the EPS exposure to ciprofloxacin. On the other hand, because of the release of EPS and the decay of filaments, soluble microbial products (SMP), particularly soluble polysaccharides, increased significantly in the MBR exposure to ciprofloxacin. Despite this, the results of this study show that the presence of trace contaminants in wastewater streams may play some positive roles in MBR fouling control.