Rare invasive fungal infection of the central nervous system (CNS) in children has a significant mortality rate. In this report, researchers discussed a case of CNS phaeohyphomycosis caused by the fungus Cladophialophora bantiana, which caused a kid to deteriorate neurological function gradually. They reviewed the current literature and discussed her clinical presentation, medicinal and surgical therapy, and outcomes. A young girl of 9 was brought in after experiencing a sudden onset of headaches, ophthalmoplegia, and ataxia. Initial infection workup involving serial cerebrospinal fluid culture for fungi was negative. Over the course of 2 months, she experienced a steady loss in her mental and physical capacities, and imaging showed that her meningitis, ventriculitis, and cerebritis were getting worse. Last but not least, plasma metagenomic next-generation sequencing uncovered Cladophialophora metagenomic next-generation sequencing (mNGS). C. bantiana infection was verified by sampling fluid from the 4th ventricle. Due to the severity of her condition, a curative operation was out of the question. Several rounds of surgical debridement and antifungal treatment, including intraventricular amphotericin B, were necessary for her recovery. Although she still has neurologic abnormalities 3 years after her diagnosis, she is nonetheless alive because of rigorous surgical and medicinal therapy. Thus far, investigators were only aware of a few reported cases of juvenile CNS phaeohyphomycosis, and this case was the first to have the etiologic agent identified by plasma mNGS. Phaeohyphomycosis of the central nervous system is a potentially fatal infection. Surgical resection and antifungal treatment are the gold standards for treatment. Intraventricular antifungal treatment is an option for patients with recalcitrant ventriculitis. The gold standard for diagnosis is to obtain a CNS sample for pathogen identification and susceptibility testing directly, but plasma mNGS may speed up the process.