Malignant germ cell tumors are rare tumors of childhood accounting less than 3% of pediatric malignancies, and endodermal sinus tumor (EST) is the most common histological subtype. The vagina is an extremely rare site for germ cell tumors (GCT). A one-year female was admitted with history of bleeding per vagina. She had pallor and a mass was palpable anteriorly on rectal examination. Magnetic Resonance Imaging (MRI) showed a tumor mass at the junction of cervix and vagina and biopsy was suggestive of a vaginal EST. The serum alpha fetoprotein (AFP) was elevated. She underwent vaginohysterectomy. The tumor was excised in toto and patient received four courses of cisplatin, etoposide and bleomycin. At one year of follow up, patient was symptom free and serum AFP remained at normal level. EST of the vagina is a rare, highly malignant GCT that exclusively involves children less than 3 years of age. It is both locally aggressive and capable of metastasis. Even though more conservative surgery is advised to maintain sexual and reproductive function, at times, radical surgery is mandatory depending on the infiltration of the tumor to the surrounding structures. Simple tumor excision is not sufficient, as residual cells induce recurrence and make chemotherapy ineffective. The serum AFP level is a useful marker for diagnosis and monitoring the recurrence of vaginal EST in infants.