The currently applied disinfection methods during water treatment provide effective solutions to kill pathogens, but also generate harmful byproducts, which are required to be treated with additional efforts. In this work, an alternative and safer water disinfection system consisting of silver nanoparticle/multiwalled carbon nanotubes (Ag/MWNTs) coated on a polyacrylonitrile (PAN) hollow fiber membrane, Ag/MWNTs/PAN, has been developed. Silver nanoparticles of controlled sizes were coated on polyethylene glycol-grafted MWNTs. Ag/MWNTs were then covalently coated on the external surface of a chemically modified PAN hollow fiber membrane to act as a disinfection barrier. A continuous filtration test using E. coli containing feedwater was conducted for the pristine PAN and Ag/MWNTs/PAN composite membranes. The Ag/MWNT coating significantly enhanced the antimicrobial activities and antifouling properties of the membrane against E. coli. Under the continuous filtration mode using E. coli feedwater, the relative flux drop over Ag/MWNTs/PAN was 6%, which was significantly lower than that over the pristine PAN (55%) at 20 h of filtration. The presence of the Ag/MWNT disinfection layer effectively inhibited the growth of bacteria in the filtration module and prevented the formation of biofilm on the surface of the membrane. Such distinctive antimicrobial properties of the composite membrane is attributed to the proper dispersion of silver nanoparticles on the external surface of the membrane, leading to direct contact with bacterium cells.