Thrombophlebitis of the portal venous system (PVS) with superimposed bacterial infection (septic pylephlebitis) is an extremely rare complication of Crohn's disease (CD), and therefore diagnosis of septic pylephlebitis is difficult without high clinical suspicion. A 16-year old male patient who was diagnosed with CD 3 months earlier was admitted with recurrent fever and abdominal pain. CD activity had been well controlled with conventional medical treatment during a follow-up period. Abdominal contrast-enhanced computed tomography showed massive thrombosis in the PVS without evidence of intra-abdominal infection, and blood cultures were positive for Streptococcus viridians. There was no evidence of deep vein thrombosis or pulmonary thromboembolism, and all laboratory tests for thrombophilia were normal. Based on these findings, the patient was diagnosed with septic pylephlebitis complicated with CD, and was successfully treated with intravenous antibiotic therapy combined with anticoagulation. This case suggests that early comprehensive evaluation is crucial for immediate diagnosis and proper treatment of septic pylephlebitis in patients with CD who present with fever and abdominal pain of unknown origin, even with stable disease activity and absence of other intra-abdominal infections.