While the national prevalence of stunting in Indonesia has decreased, the level remains high in many districts/cities and there is significant variation. This ecological study employed aggregated data from the Basic Health Research Report and the District/City Poverty Data from 2018. We investigated the determinants of stunting prevalence at the district/city level, including autocorrelation applying the spatial autoregressive (SAR) model. The analyses revealed stunting prevalence above the national average in 282 districts/cities (54.9%), i.e. ≥30% in 297 districts/cities (57.8%) and ≥40% in 91 districts/cities (17.7%). Autocorrelation was found between Sumatra, Java, Sulawesi as well as Bali, East Nusa Tenggara and West Nusa Tenggara (Bali NTT NTB). The SAR modelling revealed the following variables with significant impact on the stunting prevalence in various parts of the country: closet defecation, hand washing, at least four antenatal care visits during pregnancy, poverty, immunisation and supplementary food for children under 5 years.