The development of septic thrombosis due to central venous catheterization is relatively rare and difficult to diagnose. The associated morbidity and mortality is high if medical therapy fails. We report a 51-year-old male who presented with fever and persistent Staphylococcus aureus septicemia. The same pathogen was also isolated from the tip of his Hickman catheter. Enhanced computed chest tomography (CT) demonstrated thrombosis of the superior vena cava and septic pulmonary embolization. The treatment included early removal of the infected catheter and intravenous broad-spectrum antibiotics. However, further complications including infective endocarditis of the tricuspid valve, septic pulmonary embolization and acute hypoxic respiratory failure were encountered. The patient ultimately expired due to refractory septic shock and multiple organ failure. This case reminds us that medical therapy may be insufficient and surgical thrombectomy and removal of the infected vein may be necessary.