Among uterine cystic tumors, uterine cyst arising from secondary Müllerian epithelium is exceedingly rare. A 45-year-old woman presented with pelvic cystic mass, which was initially diagnosed as a paraovarian cyst by ultrasound and magnetic resonance imaging. At laparoscopy, the cyst proved to be a pedunculated uterine cyst, which was easily resected. Histologically, the cyst wall was lined by fallopian epithelium and positively stained for WT-1, estrogen receptor, and progesterone receptor. The final diagnosis was Müllerian cyst of the uterus. Preoperative diagnosis of uterine Müllerian cyst is usually impossible. Laparoscopy is useful as a minimally invasive treatment to diagnose and resect the cyst at the same time. Specific immunostaining is useful to make a definite diagnosis of Müllerian cyst of the uterus.