Background The human microbiome comprises of microbes that live on or within various sites of the human body. These diverse microbes have the potential to impact our physiology, both in health and disease. Recently, several autoimmune diseases have been associated with the alterations in patients’ microbiota, including myasthenia gravis. Thus, this study aims to understand the role of gut microbiome in myasthenia gravis (MG) development, as well as obtaining clues on the regulation of gut microbiome to modulate the disease. Methods A systematic search was conducted using predefined MeSH terms ‘myasthenia gravis’ and ‘gut microbiome’ or ‘microbiota’ in three databases (Pubmed, Ovid Medline, Scopus; from database inception to December 2019). All the journal titles and abstracts were screened based on inclusion and exclusion criteria. Studies reporting gut microbiome data in relation to gut microbiome effects were included. Studies without myasthenia gravis and/or gut microbiome data were excluded along with conference abstracts, reviews, systematic reviews, meta-analyses, and comments. Results The systematic search identified 19 articles based on the MeSH term. The duplicate records were removed and 13 articles were accessed. Three studies were eligible for the qualitative analysis according to the inclusion criteria. All the studies reported changes in the microbiota composition as compared to control groups, with significantly lower in phyla Firmicutes and Actinobacteria. MG patients were found to harbour increased of the phylum Bacteroidetes and the family of Desulfovibrionaceae. The ratio of Firmicutes/Bacteroidetes in MG patients describes an inflammatory microbiota which might cause damage to the intestinal epithelium, subsequently trigger an immune response that contributes to the immunological imbalance characteristic of autoimmune disorder. It is reported that some of these microbes were linked with acetylcholine receptor (AchR) antibody, suggesting the gut microbiome influence the onset of myasthenia gravis through classical pathogenic pathways. Conclusions These findings provide vital insight and knowledge on MG gut microbiome that could enhance the potential for future microbial-based therapies to improve the clinical outcome of MG. Figure 1 illustrates the dysbiosis of the gut microbiome in myasthenia gravis patients.