Human protothecosis is mainly a cutaneous infection caused by the Prototheca species. Prototheca wickerhamii is an established pathogen of eosinophilic meningoencephalitis in dogs, but no eosinophilic pleocytosis of the cerebrospinal fluid has been reported in human cases of meningitis. Herein, we report a case of chronic protothecosis manifesting eosinophilic meningoencephalitis in an immunocompetent boy.