Introduction: Understanding the specific geospatial variations in childhood stunting is essential for aligning appropriate health services to where new and/or additional nutritional interventions are required to achieve the Sustainable Development Goals (SDGs) and national targets.

Objectives: We described local variations in the prevalence of childhood stunting at the second administrative level and its determinants in Nigeria after accounting for the influence of geospatial dependencies.

Methods: This study used the 2018 national Nigeria Demographic and Health Survey datasets (NDHS; N = 12,627). We used a Bayesian geostatistical modelling approach to investigate the prevalence of stunting at the second administrative level and its proximal and contextual determinants among children under five years of age in Nigeria.

Results: In 2018, the overall prevalence of childhood stunting in Nigeria was 41.5% (95% credible interval (CrI) from 26.4% to 55.7%). There were striking variations in the prevalence of stunting that ranged from 2.0% in Shomolu in Lagos State, Southern Nigeria to 66.4% in Biriniwa in Jigawa State, Northern Nigeria. Factors positively associated with stunting included being perceived as small at the time of birth and experience of three or more episodes of diarrhoea in the two weeks before the survey. Children whose mothers received a formal education and/or were overweight or obese were less likely to be stunted compared to their counterparts. Children who were from rich households, resided in households with improved cooking fuel, resided in urban centres, and lived in medium-rainfall geographic locations were also less likely to be stunted.

Conclusion: The study findings showed wide variations in childhood stunting in Nigeria, suggesting the need for a realignment of health services to the poorest regions of Northern Nigeria.