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Introduction Non-tuberculous mycobacterial pulmonary disease (NTM-PD) is a chronic debilitating infection requiring prolonged multidrug therapy. Common symptoms contribute to inactivity, malnutrition and sarcopenia, and low muscle mass is associated with increased mortality. Evidence supporting exercise in NTM-PD is scarce, and no randomised controlled trial has evaluated its efficacy. This study aims to determine whether a 6-week hybrid, circuit-based exercise programme improves cardiorespiratory fitness compared with delayed intervention/usual care and to evaluate its effects on physical function, activity, pulmonary function and patient-reported outcomes.Methods and analysis This single-centre, randomised, open-label, two-arm trial will enrol 50 adults with NTM-PD, allocating them 1:1 to immediate or delayed intervention. The intervention is a 6-week hybrid circuit comprising one supervised and six home-based sessions per week, integrating aerobic, resistance and core exercises. Exercise intensity will be moderate and progressively adjusted using maximum heart rate determined by cardiopulmonary exercise testing (CPET). Adherence will be monitored through daily exercise diaries and brief nutrition education and walking training will also be provided. The primary outcome is maximal oxygen uptake (VO₂max, mL/kg/min) measured by CPET. Secondary outcomes include the 6-Minute Walk Test, 30-Second Sit-to-Stand, Short Physical Performance Battery, forced vital capacity, forced expiratory volume in 1 s, bioelectrical impedance analysis, Quality of Life-Bronchiectasis, Chronic Obstructive Pulmonary Disease Assessment Test and Hospital Anxiety and Depression Scale. Assessments will occur at baseline, postintervention and at an exploratory 6-month follow-up.Ethics and dissemination The study was approved by the Severance Hospital Institutional Review Board (IRB No. 4-2024-0147), and written informed consent will be obtained in accordance with the Declaration of Helsinki. Results will be disseminated through peer-reviewed publications and scientific meetings to inform non-pharmacological management of NTM-PD.Trial registration number NCT06488495.