A 51-year-old immunocompetent Japanese woman presented with a rare case of granulomatous amoebic encephalitis (GAE) caused by Balamuthia mandrillaris. She was brought to our hospital with epilepsy. Magnetic resonance imaging of the brain revealed a homogeneously enhanced solitary mass in the left frontal lobe. Histological diagnosis was made by a biopsy, which suggested lymphomatoid granulomatosis. After that, her neurological condition got worse. New masses were found and had spread across the whole brain. She died 2 months later of cerebral hernia. Autopsy revealed that the patient had GAE caused by Balamuthia mandrillaris. GAE is usually fatal, and is difficult to diagnose except at autopsy. Therefore, awareness of this disease is important, and earlier diagnosis and the development of a better therapeutic strategy will improve clinical outcome.