Case Report: A 34-year-old woman presented with a desire to conceive. However, she could not participate in sexual intercourse because of severe vaginal pain. In vitro fertilization (IVF) was performed, and she achieved pregnancy. Although she could have had a twin pregnancy following IVF, one fetus was aborted. Results: Dilatation and curettage (D&C) was carried out with the patient under general anesthesia. The authors found a vaginal septum, which explained the severe vaginal pain upon attempting sexual intercourse. Although they carried out D&C, they were unable to completely remove the gestational sac. Diagnostic laparoscopy was then undertaken, revealing a duplicate uterus. Conclusion: This case indicates the need to be aware of the possibility of anomalies of the vagina and uterus when patients present with a disorder in sexual function. Clinicians should carefully listen to such patients’ complaints in clinical practice.