Background: To report the life-threatening complication of a raptured heterotopic pregnancy occurring from thawed single embryo transfer. Case Report: A 33-year-old woman underwent in vitro fertilization (IVF) under a step-up regimen. After oocyte collection, blastocysts were frozen, and a single frozen-thawed blastocyst was then transferred according to the natural cycle. On day 17 after embryo transfer, an intrauterine pregnancy was confirmed. On day 28, she complained of sudden abdominal pain and ultrasonography revealed marked fluid retention in the peritoneal cavity. Emergency laparoscopy was performed, revealing hemoperitoneum and a ruptured interstitial heterotopic pregnancy (HP), which was then resected laparoscopically. Because sexual intercourse had occurred shortly before the transfer, a HP comprising a spontaneous pregnancy and a pregnancy achieved by assisted reproductive technology was assumed. The fetus in the uterus survived and was delivered. Conclusion: In this case, however, despite the single embryo transfer during the natural-cycle frozen-thawed embryo transfer process, the risk of life-threatening complication as a HP as a consequence of spontaneous pregnancy after sexual intercourse remained.