The objective of this study is to review applications of multicriteria decision analysis (MCDA) methods to provide structure for and practical insights on how MCDA methods are applied in different healthcare areas. Four databases (Embase, Medline, Web of Science, and PubMed) were searched from 1980 to February 7, 2018. A scoping review was performed to outline the most frequently applied MCDA methods, in which only case studies were considered, as the objective was to assess the applications of MCDA methods. Seventy case studies were selected. The review showed that the first real‐life application was published in 1990. With regard to areas of application, three aspects were analysed: type of health services (public or private), type of intervention (preventive, diagnostic, or treatment), and healthcare area (policymaking; resource allocation; health technology assessment; pharmaceutics; and hospital, clinical, or patient level). Data revealed that MCDA was principally used in public health services (n = 59). Three types of interventions were identified: prevention (n = 36), diagnosis (n = 32), and treatment (n = 2). An MCDA process of application was then followed to provide practical insights. During the problem‐structuring phase, results showed that processes for selecting stakeholders and criteria differed among healthcare areas. For model building, authors preferred value measurement methods and especially the analytical hierarchy process. Authors of the 70 case studies included and confirmed the usefulness of MCDA in different healthcare contexts. The stakeholders, criteria, and MCDA methods chosen differ from one study to another, answering different research objectives in different healthcare areas. This scoping review highlights the importance of each MCDA step (using Belton and Stewart's framework), from problem structuring (including the selection of stakeholders) to the model building phase (encompassing the selection of the appropriate MCDA method). We recommend structured and justified analysis so that decision makers and stakeholders can feel confident during the application process in order to make final decisions more meaningful. Further work is needed to help researchers and decision makers when choosing a suitable MCDA method.