A 75-year-old woman presented with rapidly progressive glomerulonephritis with positive results for anti-myeloperoxidase anti-neutrophil cytoplasmic antibody (MPO-ANCA). Corticosteroid therapy was successfully introduced. However, 7 months later, magnetic resonance imaging revealed marked swelling in the falx cerebri and high density regions were apparent on gallium scintigraphy, leading to diagnosis of hypertrophic cranial pachymeningitis (HCP). Symptoms improved with intensified corticosteroid therapy, but radiological examination 9 months later revealed right nasal sinus inflammation accompanied by osteolytic change. Granulomatosis with polyangiitis (Wegener's) was finally diagnosed. HCP is an important complication in MPO-ANCA-related vasculitis, and needs to be considered during the clinical course.