The 2015/2016 National Family Health Survey (NFHS-4) revealed that the prevalence of anemia among children under five years is 58% in India. Lack of nutritional supplementation and lack of health care facilities are found to be important influential factors of anemia among children. We aimed to examine district-level spatial heterogeneity and clustering of associated factors with childhood anemia in India. Geographically weighted regression was applied on the NFHS-5 data for 335 districts. Factors such as prevalence of nutritional supplementation in children and mothers, birth order, antenatal care, diarrhea in children, and stunting were found to be significantly associated. Spatial scan statistics technique identified three significant local spatial clusters of anemia. This study provides findings based on the latest available data which can further assist in the design and execution of tailor-made policies.