A 6-year-old male golden retriever, with an 8-month history of seizures and a clinical diagnosis of lymphoma in the central nervous system, was (at the owner's request) euthanized after signs of respiratory distress and shock developed. Upon postmortem examination, the diagnoses of meningoencephalitis and pneumonia were made. A histological examination of selected tissues from both the lung and central nervous system revealed a severe, acute, multifocal, amoebic, embolic pneumonia and a severe, chronic, multifocal, nonsuppurative, amoebic meningoencephalitis. Indirect immunofluorescence analysis confirmed the presence of trophozoite and cyst stages of Balamuthia mandrillaris. This is the first report of B. mandrillaris (which is a free-living amoeba) causing fatal, multifocal granulomatous amoebiasis in a dog in Australia.