Mycobacterium smegmatis is a common environmental mycobacterium that was first identified in 1884, yet is a rare pathogen in humans. The few M. smegmatis infections reported to date have been localized and have occurred in association with a primary lesion in otherwise immunocompetent individuals. To our knowledge, no case of disseminated M. smegmatis infection has ever been reported, even in patients with severe immune deficiencies. We report a case of disseminated mycobacterial infection that was diagnosed in a 3-year-old girl. The pathogen was not identified as M. smegmatis until the patient was 6 years old. Her condition gradually worsened, and she died when she was 8 years old despite appropriate antimycobacterial therapy. No other opportunistic infections were documented. Immunological investigations revealed an inherited interferon γ receptor 1 deficiency. This report identifies M. smegmatis as a new opportunistic agent that may be responsible for disseminated disease in immunocompromised individuals.