Yolk sac tumors (YSTs) are rare malignancies that originate from germ cells and rarely present with endocrine symptoms. We report a case of a 13-year-old girl with a YST manifesting as virilization.A 13-year-old girl was diagnosed with a YST with endocrine symptoms because of Leydig cells in the stroma, which were identified using hematoxylin and eosin staining and immunohistochemistry.This case suggests that clinicians should consider the possibility of YST when encountering patients with symptoms of virilization. When a YST is found to have endocrine function, a functioning stroma could present. Immunohistochemistry is useful for identifying stromal cells and performing a differential diagnosis.