An eight-year-old girl was admitted with vomiting, gross hematuria, and progressive renal dysfunction. A renal biopsy revealed endocapillary proliferative glomerulopathy and crescent formation. Immunofluorescence staining revealed diffuse granular deposits of IgG and C3. Post-streptococcal acute glomerulonephritis (PSAGN) was suspected, based on the elevated anti-streptolysin O levels, decreased serum C3 concentrations, and histologic findings. The myeloperoxidase anti-neutrophil cytoplasmic antibody (MPO-ANCA) test was positive, and the young patient gradually developed palisaded neutrophilic and granulomatous dermatitis (PNGD), orbital and paranasal sinus granulomatous neoplasms, along with intermittent nose, head, and orbital pain. Finally, she was diagnosed with the rare MPO-ANCA-associated granulomatosis with polyangiitis (GPA) superimposed on PSAGN. The patient was treated with aggressive renal replacement therapy, methylprednisolone pulse therapy, and intravenous pulse cyclophosphamide; her renal function normalized, and her pain symptoms improved.