Objectives: To estimate geographical variations of child immunisation at the regional level in Senegal, to identify individual and contextual factors that could explain these regional discrepancies, and to measure their effects. Methods: Data come from the 2015, 2016 and 2017 Senegalese Demographic and Health Survey, a national survey targeting women aged 15-49, with a questionnaire focusing on health and reproductive issues including their children's immunisation status. We restricted the analysis to children aged 12-23 months (n = 4955) and conducted a multilevel logistic regression to assess individual and contextual factors associated with complete immunisation coverage. Results: The complete immunisation coverage rate of children was estimated at 68% and ranged from 41% in the region of Kedougou to 83% in the region of Dakar. The inter-regional variance was significantly different from zero (P = 0.006) in the empty multilevel model. It decreased by more than half (57 %) after adjusting for individual factors but remained significantly different from zero (P = 0.010). Regional variations of complete immunisation rates drastically decreased and were no longer statistically significant (P = 0.343) after adjusting for the following regional factors: population density, density of hospitals, literacy rate and proportion of health facilities with an antenatal care service. Conclusions: Regarding health policies designed to improve childhood immunisation and to reduce related inequalities, our results highlight the need to take into account both individual and contextual factors, with a focus on rural and deprived areas where children are at higher risk of incomplete immunisation.