The free-living amebas Naegleria and Acanthamoeba are recognized as causal agents of central nervous system infections. Recently a third free-living ameba, Balamuthia mandrillaris, was identified as the causal agent of granulomatous encephalitis in humans. We report a case of Balamuthia encephalitis in an immunocompetent school-age girl who presented cutaneous lesions that compromised the central portion of the face. The skin biopsy revealed granulomatous lesion with positive PCR for non-tuberculous Mycobacterium. We started treatment for atypical extrapulmonary mycobacteriosis. Nevertheless, the child was readmitted six months later, with progressive neurological involvement, dying about one year after the onset of cutaneous symptoms. The brain necropsy showed the presence of B. mandrillaris cysts and trophozoites. Balamuthia mandrillaris infection should be considered in the differential diagnosis of a patient with chronic granulomatous disease with neurologic symptoms.