In this study, we evaluated the efficacy of Lactobacillus gasseri OLL2809 on endometriosis by the randomized, double-blind and placebo-controlled clinical study, especially against pain, which is one of the causative factors to decrease the quality of life. Sixty-six patients clinically diagnosed with endometriosis were enrolled in this study, 62 of which have successfully completed the trial. The tablets containing 100 mg of L. gasseri OLL2809 (active tablet, n = 29) or placebo tablets (n = 33) were ingested once a day for 12 weeks. Visual analog scale (VAS) of pain intensity at the menstrual period and verbal rating scale (VRS) of dysmenorrhea were significantly improved by the ingestion of the active tablets as compared with placebo tablets. There was no significant change of blood examination and biochemical examination of blood in the enrolled patients. Above results show that the tablet containing L. gasseri OLL2809 is effective on endometriosis, especially against menstrual pain and dysmenorrhea. Moreover, it was found that the tablet has no adverse effects. Therefore, it was suggested that the tablet containing L. gaserri OLL2809 contributes to improve the quality of life in the patients with endometriosis.