The COVID-19 pandemic has affected national healthcare systems worldwide, with around 282 million cumulative confirmed cases reported in over 220 countries and territories as of the end of 2021. The Italian National Health System was heavily affected, with detrimental impacts on preventive service delivery. Routine vaccination services were disrupted across the country during the first months of the pandemic, and both access to and demand for vaccines have decreased during the pandemic. In many cases, parents preferred to postpone scheduled appointments for routine paediatric vaccinations because of stay-at-home orders or fear of COVID-19 infection when accessing care. The objective of the current study was to assess the routine childhood vaccine coverage (VC) rates during the COVID-19 epidemic in Italy. We compared 2020 and 2019 VC by age group and vaccine type. The Italian Ministry of Health collected anonymised and aggregated immunisation national data through the local health authorities (LHAs). Results were considered statistically significant at a two-tailed p-value ≤ 0.05. VC rates for mandatory vaccinations decreased in 2020 compared to 2019 (range of VC rate decrease: −1% to −2.7%), while chicken pox increased (+2.2%) in 7-year-old children. Recommended vaccinations were moderately affected (range of VC rate decrease in 2020 vs. 2019: −1.4% to −8.5%), with the exception of anti-HPV in males, Men ACWY, and anti-rotavirus vaccination (VC increase 2020 vs. 2019: +1.8%, +4.7% and +9.4%, respectively). In the COVID-19 era, the implementation of coherent, transparent, and effective communication campaigns and educational programs on safe childhood vaccinations, together with the increase in the number of healthcare staff employed, is essential to support strategies to reinforce vaccination confidence and behaviour, thus avoiding health threats due to VPD during and beyond COVID-19 times.