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Abstract Background After the military coup in Myanmar in February 2021, the health system began to disintegrate when staff who called for the restoration of the democratic government resigned and fled to states controlled by ethnic minorities. The military retaliated by blocking the shipment of humanitarian aid, including vaccines, and attacked the ethnic states. After two years without vaccines for their children, parents urged a nurse-led civil society organization in an ethnic state to find a way to resume vaccination. The nurses developed a vaccination program, which we evaluated. Methods A retrospective cohort study and participatory evaluation were conducted. We interviewed the healthcare workers about vaccine acquisition, transportation, and administration and assessed compliance with WHO-recommended practices. We analyzed the participating children’s characteristics. We calculated the proportion of children vaccinated before and after the program. We calculated the probability children would become up-to-date after the program using inverse survival. Results Since United Nations agencies could not assist, private donations were raised to purchase, smuggle into Myanmar, and administer five vaccines. Cold chain standards were maintained. Compliance with other WHO-recommended vaccination practices was 74%. Of the 184 participating children, 145 (79%, median age five months [IQR 6.5]) were previously unvaccinated, and 71 (41%) were internally displaced. During five monthly sessions, the probability that age-eligible zero-dose children would receive the recommended number of doses of MMR was 92% (95% confidence interval [CI] 83–100%), Penta 87% (95% CI 80%–94%); BCG 76% (95% CI 69%–83%); and OPV 68% (95% CI 59%–78%). Migration of internally displaced children and stockouts of vaccines were the primary factors responsible for decreased coverage. Conclusions This is the first study to describe the situation, barriers, and outcomes of a childhood vaccination program in one of the many conflict-affected states since the coup in Myanmar. Even though the proportion of previously unvaccinated children was large, the program was successful. While the target population was necessarily small, the program’s success led to a donor-funded expansion to 2,000 children. Without renewed efforts, the proportion of unvaccinated children in other parts of Myanmar will approach 100%.