This paper assesses the prevalence of stunting and its potential determinants using data from the Demographic and Health Surveys (DHS) conducted in Rwanda and Burundi in 2010. Selected child, mother, and household characteristics are described for rural and urban areas in each country and the logistic regression model is constructed for each setting independently. The results show that male sex and increasing age are associated with stunting in rural and urban children in both the countries. The child’s size at birth is associated only in urban Rwanda and rural Burundi, and the fact that the child has not received vitamin A supplementation or vaccination only in rural settings (Rwanda and Burundi, respectively). Regarding mother’s characteristics, young age is a stunting potential risk factor in all settings except in urban Rwanda, and mother’s low educational levels in all settings except for rural Rwanda, although the mother’s working status has a significant impact on the child’s nutritional status only in this country. Finally, low socioeconomic status at the household level is associated with chronic malnutrition only in rural settings, and the mother’s partner’s education and no sanitation in rural Burundi and urban Rwanda, respectively. Nutrition programming should differentiate between urban and rural contexts within a country. The 1000 days approach that advocates interventions from conception to the second birthday of the child seems to be relevant as mother’s characteristics show a strong correlation with her child’s nutritional status. In rural areas in both countries, access to health services should be enhanced.