OBJECTIVE: To examine changes in vaccination of children younger than 1 year during the coronavirus disease 2019 (COVID-19) pandemic (March 2020-August 2021) in Haiti, Lesotho, Liberia and Malawi. METHODS: We used data from health management information systems on vaccination of children aged 12 months or younger in districts supported by Partners In Health. We used data from January 2016 to February 2020 and a linear model with negative binomial distribution to estimate the expected immunization counts for March 2020-August 2021 with 95% prediction intervals, assuming no pandemic. We compared these expected levels with observed values and estimated the immunization deficits or excesses during the pandemic months. FINDINGS: Baseline vaccination counts varied substantially by country, with Lesotho having the lowest count and Haiti the highest. We observed declines in vaccination administration early in the COVID-19 pandemic in Haiti, Lesotho and Liberia. Continued declines largely corresponded to high rates of COVID-19 infection and discrete stock-outs. By August 2021, vaccination levels had returned to close to or above expected levels in Haiti, Liberia and Lesotho; in Malawi levels remained below expected. CONCLUSION: Patterns of childhood immunization coverage varied by country over the course of the pandemic, with significantly lower than expected vaccination levels seen in one country during subsequent COVID-19 waves. Governments and health-care stakeholders should monitor vaccine coverage closely and consider interventions, such as community outreach, to avoid or combat the disruptions in childhood vaccination.