Heterotopic pregnancy is a well-established complication of assisted reproductive technology. We report a case of intrauterine pregnancy combined with abdominal pregnancy diagnosed at 12 weeks in a 37-year-old nulliparous woman. Following surgical resection of the ectopic, implantation of hemorrhagic ectopic trophoblastic tissue onto bowel serosa, mesentery and omentum persisted. Due to the high risk of additional bleeding, systemic methotrexate was administered to the patient. The intrauterine pregnancy progressed well and a live infant was born at 27+3 weeks. In such difficult cases, systemic methotrexate appears to have therapeutically helpful effects at low dosing regimens without immediate fetal toxicity.