INTRODUCTION: Low-income and underserved populations, especially racial and ethnic minorities, experience health disparities linked to social determinants. The COVID-19 pandemic amplified these disparities, necessitating effective strategies to address structural racism and related factors. Vaccination, crucial for mitigating infectious diseases, including COVID-19 and influenza, remains challenging among underserved populations. Community health worker (CHW) interventions show promise in addressing these disparities but have not undergone rigorous evaluation with a randomized controlled trial to increase vaccination uptake among underserved populations. This study develops and evaluates a CHW vaccination behavior (CHW-VB) intervention to increase COVID-19 and influenza vaccination among adult patients in primary care settings. METHODS: Tailoring of the Boost Your Health (Refuerza tu Salud) intervention is grounded in behavior change theory and integrates input from a Community Advisory Board. The study employs a patient randomized controlled trial design to test the effectiveness the CHW-VB intervention compared with usual care across six Federally Qualified Health Centers (FQHCs) in New York. Patients are being screened for eligibility (vaccinated but not up to date with the COVID-19 vaccine and have at least one of seven common chronic illnesses) and 800 are assessed at baseline, three, and six months. Outcomes include COVID-19 vaccine (primary) and influenza vaccine (secondary) uptake. The study also evaluates intervention implementation using the RE-AIM model. CONCLUSION: Boost Your Health aims to increase COVID-19 and influenza vaccination among racially/ethnically diverse, underserved populations with chronic illness through the CHW-VB intervention, targeting critical gaps in vaccination uptake to reduce health disparities and increase health equity. TRIAL REGISTRATION: (ClinicalTrials.govNCT06156254).