The composition of the gut microbiota depends on many factors, including our lifestyle, diet, metabolism, antibiotic use and hygiene. The contribution of these factors in shaping the gut microbiota and the subsequent effects on the prevention and development of stroke has been under intense investigation. Furthermore, several reports have uncovered the impact of stroke on intestinal dysfunction and gut dysbiosis, highlighting the delicate interplay between the brain, gut and microbiome following this acute brain injury. Despite our growing appreciation of the gut microbiota in shaping brain health, the immune system, host metabolism and disease progression, its therapeutic capability in stroke is yet to be fully exploited. This review will explore the microbiota-gut-brain axis in stroke, and examine the potential role of the gut microbiota in the onset, progression and recovery phase of stroke.