Clear cell variant of invasive urothelial carcinoma is an extremely rare tumor. Here, we report a case of clear cell variant of invasive urothelial carcinoma of the ureter. A 59-year-old man, who complained of gross hematuria was referred to our hospital for precise examination and treatment. Computerized tomographic scanning confirmed the presence of a tumor in the right lower ureter. Urine cytology was positive. He had undergone retroperitoneoscopy-assisted right radical nephroureterectomy. Typical urothelial carcinoma with partial clear cell appearance made it difficult to make a precise pathological diagnosis and immunohistochemical stain helped to diagnosis the case as clear cell variant of invasive urothelial carcinoma. To our knowledge this is the first case of clear cell variant of invasive urothelial carcinoma of the ureter in the world.