Introduction: Medical decision-making in oncology is a complicated process and to date there are few studies examining how patients with cancer make choices with respect to different features of their care. It is also unknown whether patient choices vary by geographical location and how location could account for observed rural and metropolitan cancer differences. This paper describes an ongoing study that aims to (1) examine patient and healthcare-related factors that influence choices of patients with cancer; (2) measure and quantify preferences of patients with cancer towards cancer care using a discrete choice experiment (DCE) and (3) explore preference heterogeneity between metropolitan and rural locations. Methods and analysis: A DCE is being conducted to understand how patients with cancer choose between two clinical scenarios accounting for different patient and healthcare-related factors (and levels). Preliminary qualitative research was undertaken to guide the development of an appropriate DCE design including characteristics that are important and relevant to patients with cancer. A fractional factorial design using the D-efficiency criteria was used to estimate interactions among attributes. Multinomial logistic regression will be used for the primary DCE analysis and to control for sociodemographic and clinical characteristics. Ethics and dissemination: The Barwon Health Human Research Ethics Committee approved the study. Findings from the study will be presented in national/ international conferences and peer-reviewed journals. Our results will form the basis of a feasibility study to inform the development of a larger scale study into preferences of patients with cancer and their association with cancer outcomes.