Fecal microbiota transplantation ( FMT) is a therapeutic method in which microorganisms are transplanted from healthy donors’ feces into the gastrointestinal tract of patients, to directly change their intestinal microbiota, normalize its composition, and achieve therapeutic effects. Chronic diarrhea is closely associated with the gut microbiota and an imbalance in the gut microbiota can lead to the occurrence and progression of chronic diarrhea. FMT is an effective approach for the treatment of chronic diarrhea. This review summarizes the relationship between chronic diarrhea and the gut microbiota and considers research advancements and applications of FMT technology for managing chronic diarrhea. We also address the prevailing challenges and future prospects, to provide a reference for further studies of FMT for the treatment of chronic diarrhea.