Fungal infections develop slowly in immunocompetent patients and rarely a severe disease, however, they progress rapidly and usually prove fatal in immunocompromised patients. Early diagnosis and treatment of fungal infections is essential to survival of immunocompromised patients. We report a 33-year-old woman with systemic lupus erythematosus undergoing immunotherapy infected with combined invasive pulmonary aspergillosis and pulmonary cryptococcosis diagnosed by video-assisted thoracic surgery lung biopsy and she was successfully treated as a result of early diagnosis and treatment.