Background: Gynecologic neuroendocrine carcinoma is rare. There is no case report of secondary small cell vaginal cancer after operative therapy for endometrial cancer. Case: A 51 year-old patient was treated by operative therapy for endometrial cancer stage IA (pT1aN0M0). After 9 months' post-treatment, the patient visited the hospital with abnormal bleeding, and a necrotic lesion in the left upper third of the posterior vaginal wall was detected near the vaginal cut edge. Biopsy of this tumor revealed neuroendocrine carcinoma, the patient was diagnosed with small cell carcinoma of the vagina stage I (pT1NXM0) by following operative resection. The patient received chemotherapy with irinotecan and cisplatin. After eleven months of follow-up, the patient remains alive without recurrence. Conclusion: In case of small cell vaginal cancer, chemotherapy regimen with irinotecan and cisplatin should be considered as a therapeutic option.