Background Low-risk vaginal embryonal rhabdomyosarcoma (ERMS) requires no radiotherapy (RT) for local control. Case summary A 32-month-old girl presented with an exophytic vaginal botryoid mass, which was confirmed of be ERMS. She was given two courses of vincristine, topotecan, and cyclophosphamide (VAC) as neoadjuvant therapy, after which she underwent a hysteroscopy and conservative resection of the vaginal lesion with a negative margin. She was diagnosed with low-risk ERMS (stage I, subgroup A and Group I) and was discharged after another four courses of VAS. However, twenty-eight months after the last treatment, she presented with a giant mass protruding through the vaginal introitus, which was confirmed to be a recurrence of ERMS. Despite multiple rounds of therapy, the patient died 39 months after her diagnosis, at 5 years of age. Conclusion When making the decision to eliminate RT for low-risk vaginal ERMS patients, the risk of local recurrence should be considered and emphasized.