The study aimed to assess the prevalence and the determinants of incomplete childhood vaccination in Nigeria. The data for this study was the 2018 Nigeria Demographic and Health Survey. Multivariable multilevel logistic regression analysis techniques using Stata statistical software (version 13) were used in analyzing the data of 5,384 children aged 12-23 months old. About 69.6% of the children were incompletely vaccinated. Individual-level factors such as maternal education, household wealth were associated with incomplete vaccination. The odds of incomplete vaccination among children of mothers without education was 68% higher than those with secondary education and above (adjusted odds ratio [AOR]: (AOR = 1.68; 95% confidence intervals [CI]: 1.56-2.56). Equally children from high wealth index have reduced odds of incomplete vaccination compared to those from low wealth index (AOR = 0.58; 95% CI: 0.47-0.71). Community-level factors such as place of residence, difficulty in getting to health facility were equally associated with vaccination status. The likelihood of incomplete vaccination was 26% higher among children whose parents had difficulty reaching the health facility (AOR = 1.26; 95% CI: 1.11-1.50) than those that did not. In addition, the likelihood of been incompletely vaccinated reduced for children whose mothers live in urban areas (AOR = 0.47; 95% CI: 0.40-0.59). Incomplete childhood vaccination is prevalent in the country and associated with various individual and community factors. Program and policies aimed at improving childhood vaccination uptake should target the identified factors.