Fecal microbiota transplantation (FMT) is a medical procedure that allows to establish a stable and healthy intestinal microbiota in various diseases believed to be related to a gut dysbiosis. Currently, FMT is successfully used to treat recurrent Clostridioides difficile infection. However, in recent years there has been evidence that changes in composition of gut microbiota may also be relevant in the pathogenesis of several neuropsychiatric and neurodevelopmental conditions including Alzheimer’s disease, multiple sclerosis, Parkinson’s disease, autism spectrum disorders and schizophrenia. This review focuses on exploring the complex connection between gut microbiota and pathogenesis of these neurological conditions. It also presents current research on a possible use of FMT as a therapeutic intervention targeting the gut-brain axis.