The aim of this study was to assess the magnitude of childhood vaccination disruption and to determine the predictors of delaying childhood vaccinations during the coronavirus disease 2019 (COVID-19) pandemic among Indonesian parents. We conducted a nationwide, online, cross-sectional study. A set of questionnaires assessed the disruption of childhood vaccinations and possible explanatory variables, including demographic characteristics, current underlying disease, exposure to and confidence in COVID-19 information, perceived risk, attitude and practice on vaccination, and COVID-19 prevention practice. A multivariable linear regression was used to characterize the relationship between explanatory variables and delayed childhood vaccination. We included 1137 respondents for analysis, of which 52.6% were males and 58.4% participants aged between 31 and 50-years old. Disruption of childhood vaccination service in local health facilities was reported in 42.2% (480/1137) of respondents and 13.3% (193/1137) of respondents explained that their children could not be vaccinated because a healthcare facility temporary stopped the vaccination service. Of all respondents, 312 (27.4%) delayed vaccinating their children for a compulsory vaccination shot. Factors associated with higher odds of delaying compulsory vaccinations for children were employment and chronic disease status, flu vaccination status in the past year, and prior COVID-19 infection. In conclusion, there was a significant disruption of childhood vaccination practices in Indonesia during the COVID-19 pandemic. This is not only due to healthcare closures but also due to parents’ practice - delaying the compulsory childhood vaccination for their children. We urge the government to strengthen strategies to ensure childhood vaccination services are available to all children in the country during a pandemic.