Introduction Clinical decision-making is a complex process. Patient preference information regarding desirable health states should inform treatment and is critical to agreeing on goals of therapy. Cystic fibrosis (CF) is a common, inheritable multisystem disorder for which the major manifestation is progressive, chronic lung disease. Intermittent pulmonary exacerbations are a hallmark of disease and these drive lung damage that results in premature death. We suspect that clinicians make assumptions, most likely implicit assumptions, about outcomes that are desired by patients who are treated for pulmonary exacerbations. The aim of this study is to identify and quantify the preferences of patients with cystic fibrosis regarding treatment outcomes. Methods and analysis We will develop a discrete choice experiment (DCE) in collaboration with people with CF and their carers, and evaluate how patients make trade-offs between different aspects of health-related status when considering treatment options. Ethics and dissemination Ethics approval for all aspects of this study was granted by the Western Australia Child and Adolescent Health Service Human Research Ethics Committee [RGS903]. Weighted preference information from the DCE will be used to develop a multiattribute utility instrument as a measure of treatment success in the upcoming Bayesian Evidence-Adaptive Trial to optimise management of CF. Dissemination of results will also occur through peer-reviewed publications and presentations to relevant stakeholders and research networks.