We report a case of an acute stroke patient with pulmonary embolism (PE) caused by delayed-onset heparin-induced thrombocytopenia (HIT). She was treated with heparin to prevent neurological deterioration. However, 5 days after heparin had been given for 7 days, she developed PE. Heparin was re-started, but the platelet count decreased significantly, and a right ventricular thrombus appeared. She was finally diagnosed as having PE due to delayed-onset HIT because the HIT antibody was positive. When a patient develops thrombotic events during or after heparin therapy, the possibility of HIT should be considered.