Background: Healthcare settings are complex, and the decision-making process is usually complicated, too. Precise use of best evidence from different sources for increasing the desired outcomes is the result of EBM. Therefore, this study aimed to map the potential facilitators and barriers to EBM in health systems to help the healthcare managers to better implement EBM in their organizations. Methods: The present study was a scoping review (SR) conducted in 2020 based on the integration of the frameworks presented by Arksey and O'Malley (2005) and Levac et al. (2010) considering the Joanna Briggs Institute guideline (2015). These frameworks consist of 6 steps. After finalizing the search strategy, 7 databases were searched, and the PRISMA-ScR was used to manage the retrieval and inclusion of the evidence. Microsoft Excel 2013 was used to extract the data, and the graphic description was presented. The summative analysis approach was used applying MAXQDA10. Results: According to the systematic search, 4815 studies were retrieved after eliminating duplicates and unrelated articles, 49 articles remained to extract EBM facilitators and barriers. Six main aspects attitude toward EBM, external factors, contextual factors, resources, policies and procedures, and research capacity and data availability were summarized as EBM facilitators. The barriers to EBM were similarly summarized as attitude toward EBM, external factors, contextual factors, policies and procedures, limited resources, and research capacity and data availability. The streamgraphs describe that the international attention to the sub-aspects of facilitators and barriers of EBM has been increased since 2011. Conclusions: The importance of decision-making regarding complex health systems, especially in terms of resource constraints and uncertainty conditions, requires EBM in the health system as much as possible. Identifying the factors that facilitate the use of evidence, as well as its barriers to management and decision-making in the organization, can play an important role in making systematic and reliable decisions that can be defended by the officials and ultimately lead to greater savings in organization resources and prevent them from being wasted.