Balamuthia amoebic encephalitis (BAE) is a rare, fatal parasitic infection of the central nervous system, with a current mortality rate above 95%. The high fatality rate is largely attributed to atypical clinicopathological features, delayed diagnosis, and the absence of effective treatment methods, so quick recognition of this disease is vital. In this paper, we present a survivor of BAE, who was confirmed through histologic examination and metagenomic next-generation sequencing (mNGS) of brain lesions. This case, unlike most previous reports, was a successful survival case. It highlights the critical need for differential diagnosis in patients with central nervous system infectious diseases, particularly those with a history of skin lesions and patients presenting multifocal brain lesions. Moreover, mNGS could serve as a useful tool in rapid identification of causative rare pathogens. The application of decompressive craniectomy may offer treatment opportunities and improve the survival rate of BAE. The case description was followed by a review of the literatures, in order to improve clinicians' understanding of this disease.