Balamuthia granulomatous amoebic encephalitis (GAE) is a rare and highly lethal infectious disease affecting the central nervous system, caused by the Balamuthia amoeba. This article reports the case of a child with normal immune function and no apparent epidemiological risk factors. In the initial stages, routine blood tests, cerebrospinal fluid cell tests, biochemical tests, and metagenomic next-generation sequencing (mNGS) were all normal. Surgical removal of the abscess and subsequent pathological diagnosis revealed a chronic granuloma. mNGS analysis of the brain abscess fluid identified Balamuthia mandrillaris (BM), leading to the diagnosis of Balamuthia GAE, after which antiparasitic treatment was initiated. This case underscores the importance of sustained imaging surveillance in suspected cases of Balamuthia GAE.