Nontuberculous mycobacterial (NTM) infection in HIV (human immunodeficiency virus)-infected patients who have started highly active antiretroviral therapy (HAART) is well known to be one scenario of immune reconstitution inflammatory syndrome (IRIS). We encountered the first case in Japan of an HIV-infected patient with pulmonary Mycobacterium parascrofulaceum infection as IRIS. A 34 year-old man with acquired immunodeficiency syndrome (AIDS) was receiving highly active antiretroviral therapy. Lymphadenopathy was observed at the left pulmonary hilum. IRIS was suspected and thoracoscopic surgery was performed to diagnose the cause of lymphadenopathy. Granulomas were observed histologically, and M. parascrofulaceum was cultured. This organism was susceptible to Clarithromycin, rifampicin and levofloxacin. After the operation and without treatment, recurrence of M. parascrofulaceum infection was not observed. M. parascrofulaceum was isolated from several clinical specimens for the first time in 2004. To date, only five cases have been reported.