Introduction: Recent studies suggest a link between gut microbiota and neurological diseases, implicating the microbiome's role in neurological health. However, the specific alterations in the microbiome associated with migraine remain underexplored. This study aims to systematically review the existing literature to determine whether migraine patients are associated with changes in gut microbiota composition. Methods: A systematic review was conducted in accordance with the PRISMA statement. We included original empirical studies investigating the microbiome in migraine patients. Data extracted included study design, participant demographics, microbiome differences at various taxonomic levels, and measures of microbial diversity (alpha and beta diversity). The search and selection process involved four independent reviewers who assessed abstracts and full texts to ensure eligibility. The gut microbiota was evaluated using relative abundance and diversity indices. Results: Six studies, encompassing various regions including China, Korea, and Italy, were included in the analysis. The results indicated significant differences in gut microbiota between migraine patients and controls. Key findings include a reduction in Faecalibacterium, a genus known for its anti-inflammatory properties, in migraine patients, including those with chronic migraine. Conversely, Veillonella exhibited elevated abundance compared to controls. Other taxa, such as Prevotella and Parabacteroides, showed variable associations with migraine across different studies, suggesting a dysbiotic gut environment in migraine patients. Conclusion: This review highlights that migraines are associated with specific alterations in gut microbiota, including decreased microbial diversity and changes in the abundance of key taxa. These findings suggest that gut microbiota dysbiosis may play a role in migraine pathophysiology. Further research is needed to explore the potential causal relationships and therapeutic implications, particularly targeting the microbiome in migraine management.