In 2020, 149 million children under the age of five were estimated to be stunted globally. Around half of deaths among children under 5 years of age are related to under-nutrition. Objective of this study is to determine the association between safely managed sanitation and childhood stunting among under-five years old children in Myanmar. This cross-sectional analytical study was conducted in 16 townships across three regions and five states in Myanmar. Multiple logistic regressions analysis was performed to determine the associations. This study found that 327 (27.09%) under-five children were stunted among a total of 1207 children in Myanmar. Children with unsafely managed sanitation were 2.88 times more likely to be stunting compared with children who access to safely managed sanitation services (AOR = 2.88, 95% CI: 2.16 to 3.85; p-value <0.01). Other associated factors for childhood stunting were needs 1-15 minutes for water collection (AOR = 2.07, 95% CI: 1.46 to 2.94; p-value <0.01), 15-60 minutes for water collection times (AOR = 1.55, 95% CI: 1.08 to 2.23; p-value 0.02), improper waste water disposal (AOR = 1.99, 95% CI: 1.47 to 2.70; p-value <0.01), boys children (AOR = 4.49, 95% CI: 3.30 to 6.12; p-value <0.01), did not take vitamin A supplements(AOR = 1.64, 95% CI: 1.22 to 2.20; p-value <0.01), mothers height shorter than 153.4cm (AOR = 1.94, 95% CI: 1.45 to 2.58; p-value <0.01), and the lower minimal diet diversity (AOR = 1.47, 95% CI: 1.08 to 2.01; p-value 0.02). More access to safely managed sanitation facilities, technical sharing for proper waste water disposal, promoting household water supply system, health promotion for children's diet eating pattern, and regular support for Vitamin A supplementation are critical to reduce childhood stunting among children under the age of five in Myanmar.