Malignant germ-cell tumors (MGCT) are rare tumors of childhood accounting for less than 3% of pediatric malignancies. Endodermal sinus tumor (EST) forms the most common histologic subtype of MGCT. The vagina is an extremely rare site for GCTs. A 9-month-old female was admitted with a short history of vaginal bleeding, a mass protruding from the vagina, and difficulty in passing urine. She was pale, the bladder was full, and a mass was palpable anteriorly on rectal examination. Ultrasound showed an ovoid, hyperechoic mass posterior to the bladder. A biopsy revealed a vaginal EST. The serum alpha-fetoprotein (AFP) was elevated partial vaginectomy was done and the tumor was excised in toto. The patient was subsequently given six courses of cis-platinum, etoposide, and bleomycin and on follow-up continues to be free from disease. EST is the most common GCT in children. In females, it is usually encountered in the ovary. EST of the vagina is a rare, highly malignant GCT that exclusively involves children less than 3 years of age. The diagnosis is based on histology and raised AFP. Vaginal EST is both locally aggressive and capable of metastasis. Untreated patients have died within 2 to 4 months of presentation. Radical surgery leads to a loss of sexual and reproductive function. Long-term irradiation has secondary effects of sterility, aseptic necrosis of the femoral head, and abnormal growth of the pelvic bones. Partial vaginectomy with combination chemotherapy is the most recommended line of treatment. The surgery eradicates local tumor cells and makes subsequent chemotherapy more effective. Simple tumor excision is not sufficient, as residual tumor cells induce early recurrence and make chemotherapy ineffective. The serum AFP level is a useful marker for diagnosis and monitoring the recurrence of vaginal EST in infants.