Background Childhood mortality is a well-known public health issue, particularly in the low and middle income countries. The overarching aim of this study was to examine whether neighbourhood socioeconomic disadvantage is associated with childhood mortality beyond individual-level measures of socioeconomic status in Nigeria. Methods Multilevel logistic regression models were applied to data on 31 482 under-five children whether alive or dead (level 1) nested within 896 neighbourhoods (level 2) from the 37 states in Nigeria (level 3) using the most recent 2013 Nigeria Demographic and Health Survey (DHS). Results More than 1 of every 10 children studied had died before reaching the age of 5 years (130/1000 live births). The following factors independently increased the odds of childhood mortality: male sex, mother's age at 15-24 years, uneducated mother or low maternal education attainment, decreasing household wealth index at individual level (level 1), residing in rural area and neighbourhoods with high poverty rate at level 2. There were significant neighbourhoods and states clustering in childhood mortality in Nigeria. Conclusions The study provides evidence that individual-level and neighbourhood-level socioeconomic conditions are important correlates of childhood mortality in Nigeria. The findings of this study also highlight the need to implement public health prevention strategies at the individual level, as well as at the area/neighbourhood level. These strategies include the establishment of an effective publicly funded healthcare system, as well as health education and poverty alleviation programmes.