Background: Providing patient-centered care requires that patients partner in their personal health-care decisions to the full extent desired. Patient decision aids facilitate processes of shared decision-making between patients and their clinicians by presenting relevant scientific information in balanced, understandable ways, helping clarify patients' goals, and guiding decision-making processes. Although international standards stipulate that patients and clinicians should be involved in decision aid development, little is known about how such involvement currently occurs, let alone best practices. This systematic review consisting of three interlinked subreviews seeks to describe current practices of user involvement in the development of patient decision aids, compare these to practices of user-centered design, and identify promising strategies. Methods/design: A research team that includes patient and clinician representatives, decision aid developers, and systematic review method experts will guide this review according to the Cochrane Handbook and PRISMA reporting guidelines. A medical librarian will hand search key references and use a peer-reviewed search strategy to search MEDLINE, EMBASE, PubMed, Web of Science, the Cochrane Library, the ACM library, IEEE Xplore, and Google Scholar. We will identify articles across all languages and years describing the development or evaluation of a patient decision aid, or the application of user-centered design or human-centered design to tools intended for patient use. Two independent reviewers will assess article eligibility and extract data into a matrix using a structured pilot-tested form based on a conceptual framework of user-centered design. We will synthesize evidence to describe how research teams have included users in their development process and compare these practices to user-centered design methods. If data permit, we will develop a measure of the user-centeredness of development processes and identify practices that are likely to be optimal. Discussion: This systematic review will provide evidence of current practices to inform approaches for involving patients and other stakeholders in the development of patient decision aids. We anticipate that the results will help move towards the establishment of best practices for the development of patient-centered tools and, in turn, help improve the experiences of people who face difficult health decisions. Systematic review registration: PROSPERO CRD42014013241.