Mycobacterium haemophilum is a slow growing acid-fast bacillus (AFB) in the nontuberculous mycobacteria (NTM) group. M. haemophilum typically causes cervicofacial lymphadenitis in children, cutaneous diseases, septic arthritis and osteomyelitis. However, it rarely causes isolated spinal cord disease. We report the first case, to our knowledge, of isolated intramedullary spinal lesions secondary to M. haemophilum. This case involved a patient with newly diagnosed human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS). He developed significant immune reconstitution inflammatory syndrome (IRIS) during his treatment. M. haemophilum should be on the differential for isolated intramedullary spinal lesions, particularly in immunocompromised patients. Given our patient's severe IRIS, patients with HIV and M. haemophilum infection should be closely monitored for IRIS and treated aggressively. In high risk circumstances such as M. haemophilum spinal disease in patients with HIV, clinicians should consider pre-emptive treatment for IRIS.