Granulomatous amoebic encephalitis caused by Balamuthia mandrillaris is rare (63 human) cases reported worldwide) and fatal. We report a case in a five-year-old boy who had previously been well. For 18 months, he had had a slowly progressive, granulomatous mid facial lesion, but despite extensive investigation definitive diagnosis was made only with the acute onset of neurological signs in the last two weeks of life, when a brain biopsy specimen revealed amoebic trophozoites and cysts. Infection with B. mandrillaris should be considered in the differential diagnosis of chronic skin lesions with non-specific granulomatous histopathology and negative microbiological test results.