Amoebic meningoencephalitis is an unusual complication of bone marrow transplantation. We report a case of Acanthamoeba meningoencephalitis in a patient with non-Hodgkin's lymphoma after autologous stem cell transplantation. Leg weakness, fever and urinary retention developed 69 days following transplantation. The patient then developed fever, generalized tonic clonic seizure, rapid deterioration of mental functions and hypercapneic respiratory failure. Magnetic resonance imaging demonstrated a ring enhancing lesion at the level of the thoracic spines 11 and 12. Examination of the cerebrospinal fluid revealed pleocytosis. Despite empiric therapy with broad-spectrum antimicrobial agents, the patient's condition worsened and she died 11 days following admission. Autopsy findings revealed a subacute meningoencephalitis secondary to Acanthamoeba culbertsoni.