Central nervous system (CNS) disorders usually have gastrointestinal dysfunction beyond CNS symptoms, and gut microbiota dysbiosis can be found in patients with various CNS diseases. Intestinal microbiota and its metabolic products can participate in the activity of the central nervous system through peripheral nerves and immune pathways. Gut microbiota dysbiosis is closely associated with the development and progression of several CNS diseases such as Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, and multiple sclerosis. It has been reported that model animals or patients benefit from fecal microbiota transplantation (FMT). This paper reviews the research progress in FMT for CNS diseases.