A 22-year-old Japanese male, who was diagnosed with GATA2 deficiency two years ago, was admitted to our hospital complaining of a one-month history of fever and dry cough. A contrast-enhanced chest computed tomography (CT) scan revealed mediastinal lymphadenopathy. He was treated with broad-spectrum antibiotics, but this proved ineffective. Surgical lymph node biopsy was performed, and the resected mediastinal lymph node showed caseous necrosis, epithelioid cells, and macrophages histopathologically. Broad-spectrum antibiotics were administered on suspicion of nontuberculous mycobacteria (NTM) or tuberculosis lymphadenitis, and his general condition and mediastinal lymph node swelling deteriorated. At a later date, Mycobacterium kansasii was confirmed in the mediastinal lymph node culture. This case illustrates that in young patients with disseminated NTM infection or mediastinal lymphadenopathy due to NTM, GATA2 deficiency must be ruled out, and appropriate diagnosis and treatment should be considered.