BackgroundDiarrhoea is one of the leading reasons for under-five child mortality and morbidity across the globe and especially in low- and middle-income countries like India. The present study aims to investigate and identify the spatial clustering and the factors associated with diarrhoea across 707 districts of different states in India.MethodsThis study used National Family Health Survey-4 & 5 (2015–16 & 2019–21) data in India. Spatial analysis software i.e., ArcGIS and GeoDa including Moran’s statistics have been applied to detect the spatial prevalence and auto-correlation of diarrhoea among neighbourhood districts. Bivariate analysis with a chi-square test and logistic regression has been performed to identify the factors associated with the morbidity condition.ResultsThe result shows out of 2,23,785 children, 7.3 percent children suffer from diarrhoea in India. The prevalence is highest in Bihar (13.7%) and lowest in Lakshadweep (2.3%). Around 33 percent of districts have reported more than the national average level of diarrhoea prevalence. The study also found a medium to high level of autocorrelation with 0.41 Moran’s Index value and detected 69 hot-spots districts mostly from Maharashtra, Bihar, Odisha, and Gujarat. The study has also found, with an increase in children’s age as well as mother's age the prevalence of the disease decreases. The prevalence is more among male children than females. Underweight [OR = 1.08, 95% CI (1.03–1.13)] children have a greater risk of suffering from diarrhoeal diseases. The odds of children living in a pucca house [OR = 0.89, 95% CI (0.68–1.16)] are less likely to suffer from diarrhoea. On the other hand, rich economic status [OR = 0.91, 95% CI (0.86–0.97)], reduce the risk of such morbid conditions.ConclusionThe study recommends targeting the hot-spot districts with high prevalence areas, and district-level interventions by improving housing type and child nutrition status, which can help to prevent diarrhoeal diseases among children in India. Thus, the identification of hotspot districts and suggested policy interventions by the current study can help to prevent childhood mortality and morbidity, as well as to achieve the target given by Sustainable development Goals 3.2.