Background: Despite soaring healthcare costs, patient outcomes are suboptimal in the USA. Efforts to limit healthcare costs and improve quality of care have had limited success. An improved understanding of factors that influence clinical decision-making may provide insight into optimizing the quality and costs of care. The process of healthcare decision-making is contextual, complex and poorly understood. This study aims to explore the factors that influence clinical decision-making in the setting of limited evidence of effectiveness, limited or conflicting guidance, significant resource burden and variation in values and preferences.Rationale for study design: This sequential explanatory mixed methods study includes a case-based survey (quantitative phase). The results of the survey will guide the sampling and questions for the semi-structured interviews (qualitative phase). The interviews will provide an in-depth explanation of the survey results. Combining the two methods provides complementary information and deeper understanding of the phenomenon of clinical decision-making.Methods: The quantitative strand will consist of case-based surveys in the fields of neonatology and cardiology. Participants are asked to pick the best management choice for each question followed by a rating of the influence of different factors on a 7-point Likert scale. Follow-up questions explore knowledge and influence of evidence, guideline recommendations and costs on decision-making. Analysis of the survey results will inform sampling and the focus of qualitative interviews. The interviews will be analyzed using qualitative description.Discussion: To our knowledge, this is the first study using a mixed methods approach including a case-based survey of physicians practicing in diverse settings to explore the factors that influence clinical decision-making. The results of this study may assist with strategies to implement high value care resulting in improved patient outcomes and limiting costs.