Introduction Few clinical trials have investigated physiotherapy interventions to treat hypoxaemia following abdominal surgery. The objective of this study is to determine the feasibility and safety of conducting a clinical trial of physiotherapist-led non-invasive ventilation (NIV). Methods and analysis This single-centre, 50-patient, parallel-group, assessor blinded, pilot feasibility randomised controlled trial with concealed allocation will enrol spontaneously ventilating adults with hypoxaemia within 72 hours of major abdominal surgery. Participants will receive either (1) usual care physiotherapy of a single education session (talk), daily walking of 10-15 min (walk) and four sessions of coached deep breathing and coughing (breathe) or (2) usual care physiotherapy plus four 30 min sessions of physiotherapist-led NIV delivered over 2 postoperative days. Primary feasibility and safety outcome measures are; number of eligible patients recruited per week, total time of NIV treatment delivered, acceptability of treatments to patients and clinicians and incidence of adverse events. Secondary feasibility outcomes include measures of recruitment and treatment adherence. Exploratory outcome measures include change in respiratory parameters, postoperative pulmonary complications, length of hospital stay, health-related quality of life, postoperative activity levels and mortality. Ethics and dissemination Ethics approval has been obtained from the relevant institution. Results will be published to inform future research. Trial registration number ACTRN12622000839707.