Introduction: COVID-19 vaccines were rapidly developed and deployed on a large scale during a global crisis. A range of deployment strategies were used globally to maximize vaccine uptake. In this scoping review, we identify and analyze the main healthcare system and policy factors that guided and influenced COVID-19 vaccination deployment and uptake globally. Materials and Methods: JBI guidelines, Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR), and the population, concept, and context (PCC) framework were applied. Studies on individual COVID-19 vaccination factors, such as vaccine hesitancy, were excluded. The search was last conducted in May 2024 yielding 26,686 articles from PubMed, Embase, CINAHL, Scopus, and COVID-19 websites. A total of 47 articles and 3 guidance documents were included. The results of the thematic analysis were mapped to the Consolidated Framework for Implementation Research (CFIR). Results: The results found the following healthcare system and policy factors as integral to COVID-19 vaccination: types of vaccine products, healthcare workforce capacity, procurement strategies, distribution and cold-chain capacity, partnership, coordination, and leadership, information, communication, and registration strategies, delivery models, organizations, the existing health systems and policies on prioritization of at-risk groups and deployment plans. Discussion: Globally, COVID-19 vaccination programs responded to the pandemic by leveraging and reforming the existing healthcare systems, relying on strong leadership and global cooperation (such as the COVID-19 Vaccines Global Access Initiative). Deployment was enabled by effective communication and adoption of innovative technologies using data-driven policies to create high vaccine demand while overcoming limited vaccine supply and rapidly adapting to uncertainties.