We report a case of a 32-year-old man with recurrent fever, cough and left lumbago for more than one month. Computed tomography (CT) and magnetic resonance imaging (MRI) found bilateral multiple pulmonary nodules and a tumor-like mass in the left kidney. Fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) revealed increased uptake in the right pharyngeal recess along with pulmonary and renal hypermetabolic lesions. The pathologic findings of pulmonary and renal specimens were suggestive of granulomatous inflammatory changes. Further laboratory examinations showed an elevated level of serum cytoplasmic antineutrophil cytoplasmic antibody (c-ANCA) and serum proteinase 3-ANCA (PR3-ANCA). Clinical symptoms were significantly improved, and the size of pulmonary and renal lesions reduced following the use of steroids and cyclophosphamide together. Therefore, a final diagnosis of granulomatosis with polyangiitis (GPA) was made.