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Invasive fungal infection is a major threat to chronic granulomatous disease (CGD) patients. We present a rare case of invasive mycosis in a CGD boy. An 11-year-old preadolescent boy presented with fever, hypoxia, and dyspnea. Physical examination revealed left neck enlarged lymph nodes with healed scars. The chest revealed bilateral diminished air entry with bilateral coarse crackles. Peripheral blood leukocyte count was 28.260/μL with 84% neutrophil, 11% lymphocyte, and 4.4% monocyte. The patient’s condition deteriorated regardless of the empirical antibacterial against MRSA and suspected tuberculosis. A sputum sample was submitted for mycological investigation, and budding yeasts with pseudohyphae were detected in the direct smear and were isolated in pure culture using Sabouraud agar. Candida tropicalis was identified from cultural and microscopic features and confirmed by the Vitek 2 automated system. This result confirmed the invasive mycosis, obviously due to the underlying primary immunodeficiency, chronic granulomatous disease (CGD). Amphotericin was added, and he also received IV methylprednisolone for seven days. The patient improved and was weaned off oxygen with no fever. However, the patient was referred to a higher center for further workup, which confirmed CGD’s diagnosis. He is on the list for HLA-identical bone marrow transplantation (BMT).