A vaginal yolk sac tumor (YST) is a rare malignant germ cell tumor for infants and children, and it has been >50 years since the first case was reported. The treatment strategy has changed markedly in the past 50 years, from radical surgical treatment to conservative surgery combined with chemotherapy, and then to combined chemotherapy alone. The present study reports the case of a primary vaginal YST in a 13-month-old girl that was successfully treated by tumor resection combined with chemotherapy. The clinical symptoms, imaging features and treatment characteristics are described in detail, as well as the postoperative treatment. There was no local recurrence or metastasis for the 2 years of follow-up to date. A literature review was also conducted to investigate the clinicopathological features, treatment and prognosis of this tumor. Overall, surgery combined with bleomycin, etoposide and carboplatin combination chemotherapy can be an effective option for vaginal YST.