A 79-year-old man visited our hospital with a chief complaint of erythema around the urethral orifice of the glans, and a diagnosis of penile Bowen's disease was made by penile skin biopsy. Initially, local tumor resection with skin grafting from the femoral skin was performed. However, histopathological examination revealed a positive urethral margin of tumor. Since the degree of urethral lesion of penile Bowen's disease was unclear, the patient received glansectomy. Histopathological examination revealed a tumor lesion in the distal urethra, 7 mm from the external urethral orifice, and confirmed the complete resection of urethral Bowen's disease. The patient recovered well, with no definite recurrence of Bowen's disease up to 13 months after partial penectomy. Human papillomavirus 16 DNA was detected in the paraffin-embedded tumor sample, and in situ hybridization confirmed human papillomavirus 16 DNA locations in the tumor tissue. Immunohistochemistry revealed that p16-INK4a was widely expressed in the tumor tissue.