Seminal vesicle stones are extremely rare, and few cases have been reported. Treatment requires removal of the stone, generally through an open vesiculectomy. A 31-year-old man presented with perineal pain, painful ejaculation, and infertility of several years' duration. Multiple stones in the seminal vesicle duct system were diagnosed by radiologic examination. We treated the patient by seminal vesicle endoscopic stone removal, thereby obviating organ loss. The composition of the stones was whewellite. To our knowledge, this approach has not been previously reported, and our result may be encouraging for treatment of such pathologic conditions of the seminal vesicles.