Background: Stunting remains a significant global public health concern, affecting 149.2 million (22.0%) children under the age of 5 worldwide. Most of these children reside in Africa (with a 41% prevalence). In Rwanda, recent data from the 2019/2020 Rwanda Demographic Health Survey (RDHS) revealed that 33% of children under the age of 5 experience stunting with high level in rural Districts. Aim: To determine the prevalence and factors associated with stunting among children aged 6 to 59 months. Setting: The study was done in 6 sectors of rural Gisagara District, Southern Province of Rwanda. Methodology: A quantitative cross-sectional study design was used to know the participants of each sector within 6 sectors by considering the sample size of 374. The World Health Organization (WHO) Anthro software version 3.2.2 was used to determine the nutritional status of the children. SPSS 29.0 was used during analysis and significance level was below 5%. Results: This study showed that the prevalence of stunting was 35%. This study revealed that stunting was high in male gender, poor water treatment method, and children born with birth weight less than 2500 gr. Conclusion: Efforts should be made to improve nutritional status of mother and fetus during pregnancy, to encourage mothers or caregivers on water treatment methods, to eradicate undernutrition Contribution: the findings of this study align with the focus and scope of the African Journal of Primary Health Care and Family Medicine by addressing primary healthcare challenges and proposing actionable strategies to enhance family and community health.