The therapeutic use of human feces to promote host health and ameliorate disease has been sporadically reported in the annals of medicine for centuries. In the last half century, fecal microbiota transplantation (FMT), the therapeutic infusion of healthy donor fecal microbiome into an individual with disease, has gained widespread acceptance by the medical profession. This is largely due to FMT’s remarkable therapeutic efficacy in treating Clostridium difficile infection (CDI). Scientists are now exploring the therapeutic application of FMT to other gastrointestinal (e.g., inflammatory bowel disease and irritable bowel syndrome) and non-gastrointestinal disorders (e.g., autism, chronic fatigue syndrome, multiple sclerosis, Parkinson’s disease) in which a dysbiotic microbiome is thought to play a role in disease progression. The advent of advanced molecular techniques and their application to the gut microbiome has allowed us to begin unraveling the complexity of the gut microbiome. This deeper understanding has, in turn, helped us appreciate the gut microbiome’s crucial role in virtually every aspect of host functioning, including its central role in the development, structure, and functioning of the nervous system. This relationship, commonly referred to as the ‘microbiome–gut–brain axis’ (MGBA), describes the bidirectional communication, by way of biochemical signaling, that exists between the microbiome and the central nervous system. To date, most of the research on the role of the gut microbiome in the MGBA has been performed using animal studies. In this chapter, we review the wealth of experimental data supporting the role of the gut microbiome in the functioning of the nervous system, before exploring the scientific rationale for the clinical application of FMT, and its clinical use, in treating neurological diseases. Although preliminary, the promising results realized in managing these neurological conditions thus far, which represent a significant unmet need, warrant further research in this area.