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This study investigates the health impacts of transitioning from Gavi, the Vaccine Alliance, on vaccination coverage, infant and under-5 mortality, and disability-adjusted life years (DALYs) in low and middle-income countries between 2000 and 2021. As Gavi plays a critical role in supporting immunisation programmes for some of the world’s most vulnerable populations, understanding the consequences of funding withdrawal is vital for ensuring the sustainability of health gains. Using a quasi-experimental event study design, we leverage Gavi’s eligibility criteria and transition policy to compare countries phasing out of Gavi support with those continuing to receive assistance. Our analysis reveals significant short-term and medium-term negative effects of reduced Gavi support: the prevalence of children receiving no basic vaccines increased by 1.94 percentage points, infant mortality rose by 7.59 per 1000 live births, and under-5 mortality increased by 17.31 per 1000 live births. DALYs also rose by 1264 units per 100 000 population, with the most pronounced effects occurring during the accelerated transition phase. Although these adverse effects diminish several years after the transition, our findings provide robust evidence of the heightened vulnerability of health systems during the withdrawal of external aid. This study contributes to the literature by quantifying the health impacts of Gavi’s transition process and underscores the need for strengthening transition policies. Policymakers should consider a more gradual and tailored approach to aid withdrawal to ensure the continuity of critical health services and protect long-term health outcomes in transitioning countries.