Various forms of glomerular lesions have been described in primary Sjögren's syndrome (pSjS); however, myeloperoxidase (MPO)-antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis is rarely reported, and the disease onset and clinical course of ANCA-associated vasculitis (AAV) complicated by pSjS are not well understood. A 51-year-old woman was referred to our hospital because of mild proteinuria and microscopic hematuria. She fulfilled the classification criteria for pSjS. We performed a kidney biopsy; however, it revealed no characteristic findings for pSjS, vasculitis, or other autoimmune diseases, including systemic lupus erythematosus. After 9 months, urinalysis abnormalities worsened and renal function was slowly declining, and ANCA was found to be positive. A second kidney biopsy was performed, revealing MPO-ANCA-associated pauci-immune segmental necrotizing glomerulonephritis with crescent formation. Even though immunofluorescence microscopy did not reveal any positive findings, additional electron microscopy demonstrated the presence of mesangial electron-dense deposits in both kidney biopsies. Based on kidney biopsy results and sequential serum ANCA measurements, we considered that smoldering ANCA-associated vasculitis had developed in this patient as this can develop during the clinical course of pSjS. She responded well to steroid therapy. Serum measurement, especially perinuclear, ANCA levels can be useful in patients with pSjS to detect the onset of ANCA-associated vasculitis, even in the absence of acute renal deterioration or severe urinary abnormalities.