We aimed to estimate vaccination coverage and factors associated in completing schemes in children under 5 years old between 2000 and 2018. A secondary analysis was carried out on five national health surveys between 2000 and 2018 in Mexico. The sample was 53,898 children under 5 years old, where 30% of missing vaccination information was imputed using chained equations. During this period two basic vaccination schemes (CBS) were identified. For each doses and vaccines of both schemes and completed CBS, the coverage was estimated using weighted logistic regression models. Additionally, the factors associated with incomplete schemes were reported. Between 2000 and 2018, the caretakers who did not show the vaccination card went from 13.8% to 45.6%. During this period, the estimated vaccination coverages did not exceed 95%, except for BCG and marginally the first doses of vaccines against pneumococcus, acellular pentavalent, and Sabin. In the same period, the CBS estimated coverage decreased steadily and was under 90%, except for children aged 6–11 months (92.6%; 91.5–93.7) in 2000. Not having health insurance stands out as an associated factor with incomplete vaccination schemes. In conclusion, the imputation allowed to recuperate information and obtain better data of vaccination coverage. The estimated vaccination coverage and CBS do not reach sufficient levels to guarantee herd immunity, hence innovative strategies to improve vaccination must be established in Mexico.