The COVID-19 pandemic highlighted health inequities for vulnerable populations and the need for more equitable care and access to vaccination. This article described the implementation of a COVID-19 vaccination program for undocumented migrants in a regional academic center of general medicine and public health (Unisanté). The vaccination program's specific components included: triple coordination between the health authorities, the regional center and community partners, a walk-in and free service, no health insurance required, qualified nursing and administrative staff with previous experience with vulnerable populations, translated information materials and interpreters, a guarantee of confidentiality and a widespread communication campaign within the communities. In total, 2'351 undocumented migrants from 97 nationalities received at least one dose of mRNA COVID-19 vaccine (Spikevax) and 2242 were considered fully vaccinated. Although it was hard to assess its global effectiveness, the program vaccinated a significant number of undocumented adult migrants in the Canton of Vaud. The difficulties linked to the pandemic context, the heavy workload for healthcare staff and the limited resources were overcome by strong collaborations between the different actors involved throughout the program. Targeted public health policies, such as vaccination programs for undocumented migrants, are essential to guarantee equitable care, especially in pandemic times.