Background Childhood stunting remains the most challenging consequence of undernutrition because it is associated with suboptimal brain development and the subsequent increased risk of metabolic diseases and decreased earnings in adult life. The Sambas District in Indonesia has a high prevalence of stunting (28.4%), followed by underweight (25.5.%) and wasting (14.4%) among children, as well chronic energy deficiency (27%) and anemia (62%) among pregnant women. The present study sought to determine significant factors in childhood stunting with a focus on maternal and child nutrition and prenatal and postnatal determinants. Methods This prospective, repeat, cross-sectional study investigated factors associated with stunting among 559 infants age 0–11 months in Sambas District, Indonesia. Anthropometric measurements were performed by trained enumerators. Data from a 2016 survey of pregnant women and a 2017 survey on mothers and their children were used for postnatal data collection to quantify the prevalence of stunting at age 0–11 months. Using 20 potential predictors of stunting categorized by household characteristics, maternal characteristics, antenatal care services, and child characteristics, logistic regression analysis was conducted to assess the adjusted association between stunting and these factors. Results Of 559 children analyzed, 20.8% were stunted. In the model with low birth weight (LBW) as predictor for stunting, the odds of stunting increased significantly among children who weighed <2.500 g at birth; children who had diarrhea in the past 2 weeks and children who had incomplete basic immunization coverage as infants age 9–11 months. In model without LBW, the odds of stunting increased significantly among children who had preterm at birth, short maternal stature and children who had incomplete basic immunization coverage for 9–11 months infants. Conclusions Postnatal factors—preterm birth, low birth weight, diarrhea and complete basic immunization coverage—were associated with infant stunting in Sambas District, Indonesia. The prenatal factors such as short maternal stature were significant in the multivariate model. Policy makers, especially in the government, should recommend measures focused on those prenatal and postnatal factors to prevent stunting in children and to avoid the sequelae of childhood stunting in adult life. Copyright: © 2021 Sartika et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.