The continued depletion of fresh drinking water resources throughout the world has increased the need for a variety of water treatment and recycling strategies. Conventional wastewater treatment processes rely on extensive chemical post-disinfection to comply with the stringent microbiological safety for water reuse. When well designed and operated, membrane bioreactors (MBRs) can consistently achieve efficient removals of suspended solids, protozoa and coliform bacteria. Under optimal conditions, MBR systems can also significantly remove various viruses and phages. This paper provides an in-depth overview of the mechanisms and influencing factors of pathogen removal by MBR and highlights practical issues, such as reduced chemical disinfectant dosing requirements and associated economic and environmental benefits. Special attention has been paid to the aspects, such as membrane cleaning, membrane imperfections/breach and microbial regrowth, in the distribution system on the overall pathogen removal performance of MBR.