Available data highlights the significant impact of the COVID-19 pandemic on global vaccination trends. Despite this, comprehensive evaluations of these changes at the European level are still scarce. This study examines coverage for diphtheria, tetanus, and pertussis (DTP) and measles-containing vaccines (MCV) in the WHO European Region from 2000 to 2022. Vaccination coverage data, defined as the percentage of surviving infants who received the first and third doses of DTP (DTP1 and DTP3) and the first and second doses of MCV (MCV1 and MCV2), were extracted from UNICEF databases. Joinpoint regression analysis was employed to identify joinpoints in the time series and to estimate Annual Percent Changes (APCs) and Average Annual Percent Changes (AAPCs) over predefined timeframes. The coverages for DTP1 and MCV1 exhibit a similar trend, overall characterized by four joinpoints, one of which is in 2019. In contrast, the coverage for DTP3 does not show a significant temporal trend and lacks joinpoints, while the vaccination coverage for MCV2 shows a steadily increasing trend, with three identified joinpoints. A comparative analysis with the pre-pandemic period reveals a significant increase in the number of countries characterized by a decreasing trend during the pandemic period for all considered vaccination coverages, as indicated by the negative AAPC values. These results highlight the effect of the pandemic on childhood vaccination coverage. Compared to a mere descriptive analysis, the temporal analysis of trends using joinpoint regression provides significant opportunities to identify variations in vaccination coverages and pinpoint areas for intervention in future vaccination strategies.