A 35-year-old woman with a history of infertility, was presented to our hospital because of impaired consciousness and cerebellar ataxia, 14 days after in vitro fertilization. She received an embryo transfer under controlled ovarian hyper-stimulation. Magnetic resonance images revealed acute infarction in the cerebellum and brainstem. Magnetic resonance angiography showed a basilar artery occlusion at the end point. Following immediate intravenous rt-PA treatment, the symptoms disappeared completely. A transesophageal echocardiography revealed an atrial septal defect with a continuous left to right shunt. In addition, a Valsalva maneuver trans-esophageal echocardiography with injected saline showed the presence of jet bubbles in the left atrium crossing via the atrial septal defect. She was diagnosed with paradoxical cerebral embolism. Anticoagulant therapy was continued and she gave birth to a healthy baby. Deep vein thrombosis was associated with the ovarian hyper-stimulation syndrome that occurred during infertility treatment. As anti-phospholipid antibodies were weakly positive, the possibility of anti-phospholipid antibody syndrome was suggested. If a woman of childbearing age is presented because of stroke, it is important to administer initial therapy by keeping fertility in mind. Thrombolytic therapy for pregnant women should be carefully considered, because of the associated hazards; however, it is a very important treatment for maternal function after birth.