Squamous cell carcinoma of the anal canal in children is rare. To date, the etiology and outcome of this condition have been not fully understood. Here, we report an 11-year-old child with anal canal cancer who had concomitant disorders of sex development. Radiotherapy followed by salvage surgery achieved disease-free survival of 3 years. Since overexpression of cell cycle regulatory protein p16 was immunohistochemically evident in tumor tissue, human papillomavirus infection was considered as a causative factor in the carcinogenesis.