Thrombopoietin receptor agonist (TPO-RA) is effective for aplastic anemia (AA) and idiopathic thrombocytopenic purpura (ITP). However, the risk of thrombosis during ITP treatment with TPO-RA is higher than without TPO-RA. It is unclear whether TPO-RA increases the risk of thrombosis in patients with AA. We report a case of a 66-year-old female with severe AA having paroxysmal nocturnal hemoglobinuria (PNH) clones in the peripheral blood who developed ischemic colitis after three days of starting eltrombopag. Contrast-enhanced computed tomography showed ischemic colitis and contrast enhancement defect in the left atrial appendage, which indicated a thrombus in the heart. Stopping eltrombopag and providing supportive care improved her symptoms, and her blood cell counts gradually increased. Thrombosis should be considered when TPO-RA is administered during the immunosuppressive treatment of AA.