The incidences of infection with Mycobacterium tuberculosis and Cryptococcus neoformans in immunocompromised patients have increased, but there are few documented cases of their coexistence. We present the case of a 9-year-old female with systemic lupus erythematosus (SLE), treated with prednisone and cyclophosphamide, who was admitted to the emergency department with a 2-week history of fever, headache, malaise, fatigue, and diplopia 3 years after diagnosis. Physical examination showed limitation of abduction of the right eye, Kernig and Brudzinski signs, and hyporeflexia. Magnetic resonance imaging showed hyperdense lesions located in the caudate nucleus, and lumbar puncture showed pleocytosis, a low glucose level, and increased protein level. Cerebrospinal fluid culture identified C. neoformans and PCR detect M. tuberculosis. Treatment was started with isoniazid, rifampin, pyrazinamide, ethambutol, and amphotericin B. We found two similar reports in adults, but no data were found for either pediatric or SLE patients.