BACKGROUND: Airway clearance techniques (ACTs) for individuals with bronchiectasis are routinely prescribed in clinical practice and recommended by international guidelines, especially during an acute exacerbation. However, there is limited evidence of the efficacy of these techniques during an exacerbation to improve sputum expectoration, health-related quality-of-life (HRQOL) or exercise tolerance. The primary aim of this study is to compare the effects of the active cycle of breathing technique (ACBT), oscillating positive expiratory pressure (O-PEP) therapy, and walking with huffing on sputum expectoration for adults hospitalised with an acute exacerbation of bronchiectasis. Secondary aims are to compare the effects of these interventions on HRQOL, health status, exacerbation rates and hospital admissions in a six-month period following hospital discharge. METHODS: This multi-centre randomised controlled trial will recruit adults with an acute exacerbation of bronchiectasis requiring hospital admission. Participants will be randomised to receive one of three interventions: ACBT, O-PEP therapy, and walking with huffing. Outcome measures including sputum volume during and 1-h post ACT session, and 24-h sputum, as well as health status, HRQOL and exercise capacity will be completed during inpatient stay on day 2 and day 6 of admission, and within 24 h of hospital discharge. Time to first exacerbation, and time to first hospitalisation will be monitored via monthly phone calls for six months post hospital discharge. Health status and HRQOL will be assessed after discharge at two and six months, and exercise capacity will be assessed at six months post hospital discharge. DISCUSSION: Despite recommendations regarding the importance of ACT for individuals with bronchiectasis during an acute exacerbation, there is a gap in the literature regarding effectiveness of ACT when undertaken by individuals in this clinical state. This study will add to the evidence base regarding the effectiveness of commonly implemented ACTs during a hospital admission with an exacerbation of bronchiectasis. Additionally, it will contribute to knowledge of the long term effects on important and patient-centred outcomes, including incidence of future exacerbations, and HRQOL, which has not been previously established. Trial registration Registered on the Australian and New Zealand Clinical Trials Registry (ACTRN12621000428864).