Background Despite the multiple initiatives implemented to reduce stunting in Ecuador, it continues to be a public health problem with a significant prevalence. One of the most affected groups is the rural indigenous population. This study aimed to analyze the prevalence of chronic malnutrition in indigenous children under 5 years of age and its association with health determinants, focusing on one of the territories with the highest prevalence of stunting. Methods A cross-sectional study in 1,204 Kichwa indigenous children under the age of five, residing in rural areas of the counties with the highest presence of indigenous in the province of Chimborazo-Ecuador. A questionnaire on health determinants was applied and anthropometric measurements were taken on the child and the mother. Stunting was determined by the height-for-age z-score of less than 2 standard deviations, according to the World Health Organization´s parameters. Data were analyzed using bivariate and multivariate Poisson regression. Results 51.6% (n = 646) of the children are stunted. Height-for-age z-scores were significantly better for girls, children under 12 months, families without overcrowding, and families with higher family income. The variables that were significantly and independently associated with stunting were: overcrowding (PR 1.20, 95% CI 1–1.44), the mother required that the father give her money to buy medicine (PR 1.33, 95% CI 1.04–1.71), the father did not give her money to support herself in the last 12 months (1.58, 95% CI 1.15–2.17), mother’s height less than 150 cm (PR 1.42, 95% CI 1.19–1.69) and the child was very small at birth (PR 1.75, 95% CI 1.22–2.5). Conclusion One out of every two rural indigenous children included in this study is stunted. The high prevalence of stunting in the indigenous and rural population is multicausal, and requires an intersectoral and multidisciplinary approach. This study identified three fundamental elements on which public policy could focus: (a) reduce overcrowding conditions, improving economic income in the rural sector (for example, through the strengthening of agriculture), (b) provide prenatal care and comprehensive postnatal care, and (c) promote strategies aimed at strengthening the empowerment of women.