Background and Objectives: Balamuthia mandrillaris granulomatous amoebic encephalitis (GAE) is a rare, frequently fatal central nervous system infection in which delayed recognition remains a major determinant of outcome. The increasing use of metagenomic next-generation sequencing (mNGS), plasma microbial cell-free DNA sequencing and targeted sequencing has changed the diagnostic pathway for unexplained encephalitis, but the survival implications of earlier molecular diagnosis remain unclear. Materials and Methods: A systematic review of peer-reviewed reports published from January 2015 to June 2026 was designed according to PRISMA 2020. Eligible records reported human B. mandrillaris GAE, encephalitis, meningoencephalitis or encephalomyelitis with extractable patient-level diagnostic, treatment or outcome information. Data were narratively synthesised because case definitions, sample types, timing of testing and follow-up were heterogeneous. Results: The evidence base consisted mainly of case reports, small case series and retrospective clinical summaries. Across recent reports, B. mandrillaris GAE commonly mimicked malignancy, tuberculosis, fungal infection, autoimmune encephalitis or bacterial brain abscess. Diagnostic delay was driven by nonspecific symptoms, ring-enhancing lesions, negative routine cultures and limited clinician familiarity with free-living amoebae. Molecular methods, particularly mNGS/NGS applied to cerebrospinal fluid, plasma, blood, brain tissue or bronchoalveolar lavage fluid, repeatedly enabled antemortem diagnosis when routine tests were unrevealing. Survival reports shared a pattern of earlier tissue diagnosis or molecular identification, neurosurgical intervention when feasible, and prolonged multidrug therapy, sometimes including miltefosine or nitroxoline. Conclusions: B. mandrillaris GAE should be considered in subacute encephalitis with mass-like or multifocal enhancing lesions and negative conventional investigations. Early biopsy or non-invasive sequencing, followed by confirmatory testing and expert-guided combination therapy, represents the most actionable strategy to reduce diagnostic delay.