Background: Amid persistent disparities in Covid-19 vaccination, we conducted a scoping review to identify multilevel determinants of Covid-19 vaccine hesitancy (VH) and undervaccination among marginalized populations in the U.S. Methods: We utilized the scoping review methodology developed by the Joanna Briggs Institute and report all findings according to PRISMA-ScR guidelines. We developed a search string and explored 7 databases to identify peer-reviewed articles published from January 1, 2020–October 31, 2021, the initial period of U.S. Covid-19 vaccine availability. We combine frequency analysis and narrative synthesis to describe factors influencing Covid-19 vaccination among marginalized populations. Results: The search captured 2,496 non-duplicated records, which were scoped to 50 peer-reviewed articles: 11 (22%) focused on African American/Black people, 9 (18%) people with disabilities, 4 (8%) justice-involved people, and 2 (4%) each on Latinx, people living with HIV/AIDS, people who use drugs, and LGBTQ+ people. Forty-four articles identified structural factors, 36 social/community, 27 individual, and 40 vaccine-specific factors. Structural factors comprised medical mistrust (of healthcare systems, government public health) and access barriers due to unemployment, unstable housing, lack of transportation, no/low paid sick days, low internet/digital technology access, and lack of culturally and linguistically appropriate information. Social/community factors including trust in a personal healthcare provider (HCP), altruism, family influence, and social proofing mitigated VH. At the individual level, low perceived Covid-19 threat and negative vaccine attitudes were associated with VH. Discussion: This review indicates the importance of identifying and disaggregating structural factors underlying Covid-19 undervaccination among marginalized populations, both cross-cutting and population-specific—including multiple logistical and economic barriers in access, and systemic mistrust of healthcare systems and government public health—from individual and social/community factors, including trust in personal HCPs/clinics as reliable sources of vaccine information, altruistic motivations, and family influence, to effectively address individual decisional conflict underlying VH as well as broader determinants of undervaccination.