Balamuthia mandrillaris and Toxoplasma gondii central nervous system infections (SNC) are rare. Early diagnosis of these infections is vital for proper treatment onset. The study describes a clinical case of an immunocompetent patient with B. mandrillaris and T. gondii cerebral infection, who had a persistently non-reactive toxoplasmosis serology, attended in a tertiary care children’s hospital. There are reports that these free-living amoebas and T. gondii can co-habit the same places in nature, and that free-living amoebas can phagocytize T. gondii oocysts, allowing them to retain their infectivity inside the amoeba. Because of this, we consider the possibility that T. gondii may have entered into the patient’s central nervous system inside the amoeba, avoiding contact with the host immune system. The patient improved after surgical resection of the cerebral lesion and antimicrobial treatment.