Meningoencephalitis caused by Acanthamoeba spp . is a rare opportunistic infection, difficult to diagnose and difficult to treat, which causes death in almost all cases. We report the neuropathologic findings of a 16-year-old girl with systemic lupus erythematosus (SLE) treated with immunosuppression who died of fulminant Acanthamoeba meningoencephalitis. Neuropathologic examination revealed multiple supratentorial and infratentorial hemorrhagic necrotizing lesions with encephalitis and vasculitis with mixed inflammatory infiltrates, fibrinoid necrosis of vessel walls, and local leptomeningitis. Acanthamoeba in the lesions may be misinterpreted as macrophages. Taking them into differential diagnostic consideration, cytological differences should be detected, and relevant additional stains for reliable differentiation of these cells can be performed. To our knowledge, this is the first published case of Acanthamoeba meningoencephalitis in a patient with SLE in Germany.