Mayer-Rokitanski-Kuster-Hauser (MRKH) syndrome is a rare disease. A 27-year-old woman was admitted for primary amenorrhea and cyclic pelvic pain. Magnetic resonance imaging (MRI) revealed bilateral Müllerian remnants with functioning endometrium and a pelvic mass considered to be an endometriotic cyst. Bilateral Müllerian remnants were removed, and right ovarian cystectomy was performed at laparoscopic surgery. Accurate evaluation before the operation and informed consent are necessary to treat patients with MRKH syndrome.