The pandemic has disproportionately impacted rural communities with a higher burden of chronic disease and COVID-19 infection. West Virginia is a rural state with a high rate of diabetes, hypertension, and COPD, which are known risk factors for severe COVID-19 and long COVID. Yet, there is a significant hesitancy regarding COVID-19 vaccination uptake in the state. The purpose of this study was to use an educational intervention to increase vaccine knowledge and vaccine acceptance in rural patients with chronic disease(s) in West Virginia. This project used an academic-community partnership comprised of researchers, practitioners, community organizations, community-engaged partners, and patient stakeholders to increase COVID-19 health literacy and increase vaccine acceptance among rural West Virginians with chronic conditions. A quasi-experimental study design was used to deliver an educational intervention by trained Health Navigators using short videos to increase COVID-19 health literacy and address participants' vaccine concerns. Eligibility included adults (18 years and older) who have at least one chronic condition. A statewide community advisory board (CAB) guided the development of the educational training curriculum and implementation strategies. An adapted version of the Exploration, Preparation, Implementation, Sustainment (EPIS) framework guided the development of the intervention. Health Navigators (n = 45) delivered the educational intervention in their local communities between November 2022 and October 2023 (project implementation is still ongoing). Intervention fidelity checks, an adaptable script, and a flow chart allowed tailoring of brief videos to address participants' specific COVID-19 questions and vaccine concerns. A validated online survey, monitored by an online Research Electronic Data Capture (REDCap) database, assessed participants' knowledge, perceived susceptibility, and vaccine intention. Health Navigators delivered the intervention to 1368 West Virginians in 52 counties (59.2% women; 61.8% without a college degree). Participants reported living with an average of 2.1 ± 1.4 chronic conditions. The mean age was 43.5 ± 18.8 years. The majority of participants (81.2%) had received the primary vaccination series, and 63.1% had at least one booster. However, 18% were unvaccinated or did not complete the primary COVID-19 vaccine series. Discussions to improve vaccine literacy focused on how the vaccine was so quickly developed and protects against variants, addressing concerns related to the safety, short- and long-term side effects, and importance of vaccine uptake for immunocompromised individuals. Participants with higher concerns were more likely to be unvaccinated and to have not completed their primary series or boosters (p < 0.001). However, the educational intervention improved the willingness of individuals who were either unvaccinated or did not complete their primary vaccine series to get vaccinated (11.4%). Our findings highlight the importance of vaccine literacy in increasing vaccination rates among rural patients with chronic diseases. Using the EPIS framework allowed us to reflect upon the challenges, ensure resilience during changing local contexts, and plan and implement a promising, cost-effective intervention in rural areas. This study provides insights into the need for tailored educational interventions based on disease status, which has implications for public health and patient care in rural and underserved communities. Academic-community partnerships can be useful for successful knowledge transfer for vaccine acceptance to reduce rural health disparities.