Wegener’s granulomatosis (WG) is a relatively rare disease characterized by necrotizing granulomatous vasculitis of the upper and lower respiratory tract and glomerulonephritis. The clinical presentation of WG can be so diverse. Therefore the list of differential diagnosis is vast. We describe here a 46-year-old male patient with severe headache and fever following saddle nose deformity operation and medpor implantation. Although the patient had no risk factors for invasive fungal rhinosinusitis (IFR) such as immunosuppression or diabetes, the macroscopic examination of the nasal cavity and pathologic examination of biopsy specimen was relevant with IFR. No fungi was examined or isolated from the biopsy specimen. Detailed investigation for other granulomatous pathologic conditions revealed C-ANCA positivity. The patient was diagnosed as WG and treated with cyclophosphamide and corticosteroids for six weeks. The patient was discharged in a good condition and recovered with this treatment. We report this case to alert physicians to the significance of considering the unusual clinicopathological features of Wegener’s granulomatosis in complicated ‘difficult-to-diagnose’ febrile patients.