Highlights • Vaginal cancer is very rare and generally only occurs in the elderly. • Stage I vaginal cancer was diagnosed in a 38-year-old patient at 13 weeks of gestation after tumor removal. • After refusing an abortion and radical surgery, the patient continued with pregnancy. • The tumor recurred and invaded the surrounding tissue, the baby was delivered, and the patient began radiation therapy. • The patient passed away 8 months after delivery due to deterioration., Background Vaginal cancer is rare, accounting for only about 2% of all cancers of the female reproductive organs, and it is a disease that is rarely encountered in routine clinical practice. Vaginal cancer is mainly treated with radiation therapy or concurrent chemoradiotherapy (CCRT). However, in stage I-II cases, when the lesion is confined to the upper third of the vagina, surgical treatment may include total hysterectomy and vaginal resection with an adequate resection margin. We report a case of stage I vaginal cancer diagnosed at 13 weeks of gestation. There are very few reports on the diagnosis and treatment of vaginal cancer during pregnancy, and it was difficult to decide on a treatment plan; therefore, we report on the course of treatment followed for this patient. Case presentation The patient was a 38-year-old woman with a history of two pregnancies and zero births. The patient had thrombocytopenia and was diagnosed highly suspicious of myelodysplastic syndrome by bone marrow biopsy, and her platelet count remained at approximately 50,000/μL. At the time of the 11-week gestational checkup, a 4-cm pedunculated tumor was found in the right posterior vaginal fornix. Transvaginal tumor resection was performed at 13 weeks of gestation, and the patient was diagnosed with stage I vaginal cancer (squamous cell carcinoma). Because vaginal cancer was confined to the posterior vaginal wall fornix, radical surgery after abortion was suggested as a treatment plan. However, the patient strongly desired to continue the pregnancy, so the policy was to continue the pregnancy and follow-up. However, at 22 weeks of gestation, a recurrent tumor was found in the posterior fornix of the vagina. The lesion had invaded the paravaginal tissue, making radical surgery impossible. At 26 weeks of gestation, an elective cesarean section was performed because of giving priority to early therapeutic intervention to her recurrent vaginal cancer, and it was decided that CCRT with cisplatin would be administered from postpartum day 1. However, because of thrombocytopenia, chemotherapy could not be co-administered, and the treatment was completed with radiation alone. The therapeutic effect was partial response, but 13 weeks after the end of radiation therapy, we observed regrowth of the recurrent tumor and emergence of pelvic lymph node metastasis. The patient received palliative treatment but died 8 months after delivery due to a generally deteriorating condition, sepsis, and disseminated intravascular coagulation. Conclusions In cases of malignant tumors associated with pregnancy, treatment policies should consider the perinatal prognosis at the same time as treatment for malignant tumors, and gynecologic oncologists, obstetricians, and neonatologists, from the standpoint of their respective specialties, should thoroughly discuss the “curative effect of treatment for malignant tumors” and the “prognosis of the child after birth” and consider the treatment plan for each case.