Systemic lupus erythematosus (SLE) is a multisystemic disease with varied clinical manifestations. Focal cortical brain infarcts and CNS infections are the most common neuropathological features reported in most studies. This report describes a 32-year-old woman who had repeated episodes of strokes over 5 years. In view of polyarthritis, oral ulcers, presence of high titres of serum antinuclear antibodies, high titres of double-stranded DNA and strokes, she was treated as SLE. Despite prolonged immunosuppressive therapy with azathioprine and pulse cyclophosphamide, she succumbed to a brainstem stroke. Complete body autopsy showed multiple cerebral cortical and brainstem infarcts with fibrinoid necrosis of the vessel wall. Renal infarction with healed vasculitis and systemic vasculitis involving small vessels was seen. Extensive thrombosis was remarkable by its absence. Active necrotizing vasculitis of cerebral and renal vessels is a rare complication of SLE, which contributed to a fatal outcome in this patient.