The objectives of this review are to identify barriers/facilitators to designing, maintaining, and utilizing rare disease patient registries (RDPRs); determine whether and how these differ among patient partners, other knowledge users (KUs), and researchers; and chart definitions of rare diseases and RDPRs. RDPRs are vital to improving the understanding of the natural histories and predictors of outcomes for rare diseases, assessing interventions, and identifying potential participants for clinical trials. Currently, however, the functionality of RDPRs is not fully optimized. To improve the quality and functionality of RDPRs, it is important to understand the barriers and/or facilitators involved in their design, maintenance, and utilization; how these might differ among patient partners, other KUs, and researchers; and to delineate the range of definitions for rare diseases and RDPRs. Evidence of any study design or format (including empirical studies, books, manuals, commentaries, editorials, guidance documents, conference abstracts, review documents, and gray literature) referencing barriers/facilitators for designing, maintaining, or utilizing RDPRs will be considered for inclusion. The review will follow the JBI methodology for scoping reviews. We will search health science databases, including the Cochrane Library, Embase, MEDLINE, the JBI EBP Database, and PsycINFO, from inception onwards, as well as gray literature using the Canadian Agency for Drugs and Technologies in Health (CADTH) Grey Matters guidance. Two independent reviewers will screen titles and abstracts and full-text documents, as well as abstract data. Disagreements will be resolved through discussion or with a third reviewer. Evidence will be synthesized descriptively and reported using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRIMSA-ScR). Open Science Framework https://osf.io/mvf9r.