The patient was a 67-year-old male who required emergency transport due to a traffic injury. Intra-abdominal hemorrhage was diagnosed and emergency surgery was performed. On day 9 after surgery, his respiratory condition aggravated and bilateral pulmonary arterial embolism and inferior vena cava thrombosis at the level from the upper to lower region of the renal vein developed concomitantly. Since the patient was under treatment with unfractionated heparin to prevent atrial fibrillation, which he had developed in the past, and was positive for antibodies against heparin-platelet factor-4 (PF4) complex, we concluded that the thrombi were formed by heparin-induced thrombocytopenia (HIT). Sepsis also developed concomitantly and methicillin-resistant Staphylococcus aureus (MRSA) was detected in blood culture. No apparent source of infection was observed on imaging, which suggested that the thrombi may have been infected through a catheter, leading to suppurative thrombophlebitis. This case serves as a reminder that heparin administration may cause thrombosis and induce suppurative thrombophlebitis.