The purpose of this systematic review was to identify potential metabolomic biomarkers of endometriosis in plasma, serum, peritoneal fluid, follicular fluid, urine, endometrial tissue samples of patients with endometriosis. Search was conducted in electronic databases including PubMed, The Cochrane Library, ClinicalTrials.gov, Embase, MEDLINE, Web of Science. Randomized controlled trials, observational, cohort and case control studies, comparing metabolomic profiles in women with laparoscopically confirmed endometriosis and women with laparoscopically confirmed absence of endometriosis were included. 17 studies were included in the qualitative synthesis. According to the results of our study, potential metabolomic biomarkers for the diagnosis of endometriosis were shown to be amino acids, including threonic acid and 3-hydroxybutyric acid, succinate, citrate, lactate, acetone, 3-hydroxybutyrate, acylcarnitines and sphingomyelins. Perturbations in metabolites levels reflect disruption of metabolic pathways in the presence of the disease. Due to the controversy of published data, further research and highlights are needed for the determination of specific metabolites.