Abstract Background Due to the social isolation measures adopted in an attempt to mitigate the risk of transmission of SARS-CoV-2, there has been a reduction in vaccination coverage of children and adolescents in several countries and regions of the world. Objective Analyze the number of doses of vaccine against Measles-Mumps-Rubella (MMR) applied before and after the beginning of mitigation measures due to COVID-19 pandemic in Brazil. Methods The data collected refer to the number of doses of the MMR vaccine applied monthly to the target population residing in Brazil: cahildren, aged 12 months (first dose) and children, aged 9 years (second dose), from April 2019 to December 2020. Differences in MMR vaccine doses from April 2019 to March 2020 (before the start of mitigation measures) and April 2020 to September 2020 (after the start of the mitigation measures) were evaluated. Spatial analysis identified clusters with a high percentage of reduction in the median of applied doses no Brazil. Results There was a reduction in the median of doses applied in the Regions North (− 33.03%), Northeast (− 43.49%) and South (− 39.01%) e nos Estados Acre (− 48.46%), Amazonas (− 28.96%), Roraima (− 61.91%), Paraíba (− 41.58%), Sergipe (− 47.52%), Rio de Janeiro (-59.31%) and Santa Catarina (− 49.32) (p < 0.05). High-high type spatial clusters (reduction between 34.00 and 90.00%) were formed in the five regions of Brazil (Moran’s I = 0.055; p = 0.01). Conclusion A reduction in the number of MMR vaccine doses was evidenced as a possible effect by the restrictive actions of COVID-19 in Brazil.