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Abstract Background An estimate of 2–3 million children under 5 die in the world annually due to vaccine-preventable disease. In Ethiopia, incomplete immunization accounts for nearly 16% of under-five mortality, and there is spatial variation for vaccination of children in Ethiopia. Spatial variation of vaccination can create hotspot of under vaccination and delay control and elimination of vaccine preventable disease. Thus, this study aims to assess the spatial distribution of incomplete immunization among children in Ethiopia from the three consecutive Ethiopia demographic and health survey data. Method A cross-sectional study was employed from Ethiopia demographic and health survey (2005, 2011and 2016) data. In total, 7901mothers who have children aged (12–35) months were included in this study. ArcGIS 10.5 Software was used for global and local statistics analysis and mapping. In addition, a Bernoulli model was used to analyze the purely spatial cluster detection of incomplete immunization. GWR version 4 Software was used to model spatial relationships. Result The proportion of incomplete immunization was 74.6% in 2005, 71.4% in 2011, and 55.1% in 2016. The spatial distribution of incomplete immunization was clustered in all the study periods (2005, 2011, and 2016) with global Moran’s I of 0.3629, 1.0700, and 0.8796 respectively. Getis-Ord analysis pointed out high-risk regions for incomplete immunization: In 2005, hot spot (high risk) regions were detected in Kefa, Gamogofa, KembataTemibaro, and Hadya zones of SNNPR region, Jimma zone of Oromiya region. Similarly, Kefa, Gamogofa, Kembatatemibaro, Dawuro, and Hadya zones of SNNPR region; Jimma and West Arsi zones of Oromiya region were hot spot regions. In 2016, Afder, Gode, Korahe, Warder Zones of Somali region were hot spot regions. Geographically weighted regression identified different significant variables; being not educated and poor wealth index were the two common for incomplete immunization in different parts of the country in all the three surveys. Conclusion Incomplete immunization was reduced overtime across the study periods. The spatial distribution of incomplete immunization was clustered and High-risk areas were identified in all the study periods. Predictors of incomplete immunization were identified in the three consecutive surveys.