Umbilical endometriosis is a very rare condition, and as far as we are aware, there have been no reported cases of its malignant transformation. Here, we report a case of clear cell adenocarcinoma arising from umbilical endometriosis in a 60-year-old woman who underwent hysterectomy for a uterine myoma at the age of 38, and who denied cyclic bleeding at the site of an umbilical cutaneous nodule correlating with menses until the age of 48. An umbilical tumor (3 cm diameter) was identified by magnetic resonance imaging and an abnormal accumulation was found only at the umbilical lesion by positron emission tomography examination. We observed endometriosis adjacent to the clear cell adenocarcinoma and transformation to carcinoma from endometriosis at the umbilical lesion histopathologically. Clear cell adenocarcinoma of the umbilicus was thought to have arisen from endometriosis; it expressed HER-2 protein and showed strong mesothelial characteristics immunohistochemically.