A 28-year-old woman presenting with fever was referred to our hospital and diagnosed as septic pulmonary embolism secondary to tricuspid valve endocarditis. Although antibiotic therapy was initiated, she further showed multiple complications including Janeway lesions and cerebral infarctions, suggestive of septic systemic embolism. Transoesophageal echocardiography detected a right-to-left shunt through a patent foramen ovale (PFO). The patient was successfully treated with surgical tricuspid valvuloplasty and PFO closure. Paradoxical systemic embolism may occur in patients with septic pulmonary embolism through the PFO.