Granulomatosis with polyangiitis (GPA) is a rheumatic auto-immune disease involved in vasculitis. It is rarely reported that anti-neutrophil cytoplasmic antibodies (ANCAs) associated with GPA would cause main tract stenosis. The current report documents a 54-year-old woman, with a history of severe cough, presented with wheezing and shortness of breath. Although she was treated with cephalosporin antibiotics for half a month, the symptoms were not alleviated. Accordingly, laboratory testing, radiology and pathology was performed at the Department of Respiratory and Critical Care Medicine, Huashan Hospital. Blood samples were tested negative for ANCAs. Chest CT revealed stenosis of the main trachea and uneven thickening of the tracheal wall. Nasal sinuses CT scanning indicated thickening of the nasal mucosa. Pathological analysis demonstrated chronic granulomatous inflammation with focal lesions. According to the classification criteria of ACR/EULAR provisional 2017, the patient was diagnosed with the ANCAs-negative GPA. Following treatment with oral prednisone only for 6 months, obstruction of main tract was significantly improved. This case study is of interest for the promotion a potentially novel therapeutic intervention for GPA associated with the absence ANCA of in clinic.