Background and Objectives: One of the essential services in health centers is vaccination programs for achieving universal health coverage. During COVID-19 pandemic, 90% of countries reported disruption in vaccination, especially in the earlier phases of the COVID-19. This is a trend study aimed to compare the vaccination coverage rate (VCR) in Under-5 children in Nasiriyah (Iraq) before and during the COVID-19 pandemic. Methods: This cross-sectional study was conducted in the city of Nasiriyah in southeastern Iraq, with data collected from 79 primary health care facilities. This study evaluated the VCR in 3 periods (2018, 2019, and 2020) using multi-level random sampling. Pertinent data were extracted from the vaccination records of 598 children for Bacillus Calmette-Guérin (BCG); pentavalent 1, 2, and 3; measles; and activated oral poliovirus vaccine (OPV) 1 and 2. Missing data were completed by telephone calls to participants' parents. Logistic regression was applied to compare and estimate the odds ratios (ORs) with 95% confidence intervals (CIs) for the association between VCR and related factors. Results: The early period of the COVID-19 pandemic (2019) showed the greatest decline in the studied vaccines. Among the vaccines studied, BCG had the highest rate in all 3 periods (100% VCR) and measles had the lowest rate (83.7%), reaching 63.6% in 2020 (P<0.001). The highest OR among all types of vaccine were found for the pentavalent-2 vaccine among city dwellers and those born in 2020 (OR=2.67; 95% CI, 1.39-5.10 and OR=2.34; 95% CI, 1.28-4.28, respectively). Conclusions: The VCR for children decreased during the COVID-19 pandemic in Iraq, and new health policies are needed to increase the coverage rate. Improving the knowledge and attitudes of parents, as well as removing barriers or risk factors, can also be effective in improving the VCR.