BackgroundImmunization is one of the most effective public health initiatives, saving millions of lives and lowering the risk of diseases such as diphtheria, tetanus, influenza, and measles. Immunization saves an estimated 2–3 million lives per year. A study of the regional variations in incomplete immunization will be useful in identifying gaps in the performance of immunization programs that are not noticed by standard vaccination programs monitoring. The primary goal of this study was to identify factors influencing child immunization status and to examine regional variations in incomplete immunization among children aged 12 to 23 months in Pakistan.MethodsFor the current study, the data were taken from the Demographic and Health Survey for Pakistan (PDHS 2017–2018). Ever-married women who had children aged 12–23 months were included in this study. The immunization status of children was used as an outcome variable. In order to determine the effects of different factors on incomplete immunization, multilevel logistic model was used. To study the geographical variation of incomplete immunization, hotspot analysis was done using ArcGIS 10.7 and SaTScan software and to identify significant predictors of incomplete immunization, GWR 4 software was used.ResultsPlace of delivery, gender of child, mother’s educational level and region were identified as significant determinants of incomplete immunization of children in Pakistan. Chances of incomplete immunization of children were found significantly lower for educated mothers (AOR = 0.52, 95% CI 0.34–0.79) and mothers who had delivered children in the health facilities (AOR = 0.51, 95% CI 0.32–0.83). Female children were more likely (AOR = 1.44, 1.95% CI 1.04–1.99) to be incompletely immunized as compared to male children. FATA (AOR = 11.19, 95% CI 4.89–25.6), and Balochistan (AOR = 10.94, 95% CI 5.08–23.58) were found at the highest risk of incomplete immunization of children as compared to Punjab.The significant spatial heterogeneity of incomplete immunization was found across Pakistan. The spatial distribution of incomplete immunization was clustered all over Pakistan. The high prevalence of incomplete immunization was observed in Balochistan, South Sindh, North Sindh, South KPK, South FATA, Gilgit Baltistan, Azad Jammu Kashmir, South and East Punjab. Drang and Harcho were identified as hotspot areas of incomplete immunization in Gilgit Baltistan. Secondary clusters with a high risk of incomplete immunization were found in regions Balochistan, Sindh and FATA.ConclusionGender biasedness towards female children, regarding complete immunization of children prevailed in Pakistan. Spatial heterogeneity was also found for incomplete immunization of children. To overcome the problem access to health facilities is the foremost step. Government should target hotspot areas of incomplete immunization of children to provide primary health care facilities by opening health care units in these areas. The government in collaboration with the media should launch awareness campaigns in those areas to convince people that complete immunization is the right of every child regardless of gender.