Background Stunting is a serious public health concern in Rwanda, affecting around 33.3% of children under the age of five in 2020. Several examples of research have employed machine learning algorithms to predict stunting in Rwanda; however, no study used artificial neural networks (ANNs), despite their strong capacity to predict stunting. The purpose of this study was to predict stunting in Rwanda using ANNs and the most recent Demographic and Health Survey (DHS) data from 2020. Methods We used a multilayer perceptron (MLP) architecture to train and test the ANN model on a subset of the DHS dataset. The input variables for the model included child, parental and socio-demographic’s characteristics. The output variable was a binary indicator of stunting status (stunted vs. not stunted). Results An overall accuracy of 72.0% on the test set was observed, with an area under the receiver operating characteristic curve (AUC-ROC) of 0.84, indicating the model’s good performance. Several factors appear as important contributors to the probability of stunting among the negative value aspects. First and foremost, the mother’s height is important, as a lower height suggests an increased risk of stunting in children. Positive value characteristics, on the other hand, emphasie elements that reduce the likelihood of stunting. The timing of the initiation of breastfeeding stands out as a crucial factor, showing that early breastfeeding initiation has been linked with a decreased risk of stunting. Conclusions Our findings suggest that ANNs can be a useful tool for predicting stunting in Rwanda and identifying the most important associated factors for stunting. These insights can inform targeted interventions to reduce the burden of stunting in Rwanda and other low- and middle-income countries.