Objective We aimed to investigate the incidence and clinical characteristics of nontuberculous mycobacterial (NTM) pulmonary disease as a complication of chronic thromboembolic pulmonary hypertension (CTEPH). Methods We conducted a retrospective study of 10 cases (5.6%) complicated by NTM pulmonary disease among 180 CTEPH patients. Results Isolated species of avium (n=5), kansasii (n=2), intracellulare (n=1), abscessus (n=1) and fortuitum (n=1) were detected. NTM-infected lesions were observed in 33 of 180 (18.3%) lung segments obtained from the 10 patients, and complete obstruction due to chronic pulmonary thromboembolism was detected in 65 of the 180 segmental pulmonary arteries (36.1%). The NTM-infected segments in the CTEPH patients were significantly associated with obstructed rather than unobstructed pulmonary artery segments [25 of 65 (38.5%) vs. 8 of 115 (6.9%), p<0.01]. Cavitary, nodular, ectatic and ground-glass lesions were seen in 14, 22, seven and four of the 180 segments, respectively. Thirteen of the 14 cavitary (92.9%) lesions were located in nonperfused segments. Five patients with NTM disease underwent pulmonary endarterectomy (PEA). Of the 18 assessable NTM-infected segments in six NTM-treated patients, 17 were located in non-perfused segments and one was located in a previously perfused segment. All NTM-infected segments improved among three segments reperfused with PEA. In contrast, only eight (57.1%) NTM-infected segments improved among 14 continuously non-perfused segments. A lower body mass index was found to be a significant risk factor for NTM disease in the CTEPH patients. Conclusion This is the first report to document NTM-disease complications in patients with CTEPH. Reperfusion in cases of NTM lesions may improve the response to NTM drug therapy.