Background: In Burkina Faso, malnutrition is a public health problem. Despite the significant drop in the prevalence of malnutrition since 2009 according to the Directorate of Nutrition, malnutrition is still a major concern with regard to its consequences. The objective of this study was to determine the factors associated with acute malnutrition in children aged 6 to 59 months in the Sabou Health District, Burkina Faso. Methods: This was a descriptive, cross-sectional study conducted among 343 children aged 6 to 59 months in Sabou Health District, Burkina Faso from August 1st to 30th, 2016. Factors associated with acute malnutrition were dietary factors, family factors, environmental factors, and infectious factors determined using SPSS version 21.0 software. The difference was statistically significant for P-value of less than 0.05. Results: The prevalence of global acute malnutrition in the district was 9.0%, of which 2.6% was severe according to the Brachial Perimeter. Several factors were associated with acute malnutrition in children under 5 years of age in the Sabou health district. Indeed, morbidity was a factor associated with acute malnutrition in children with a P-value of 0.007. The low dietary diversity experienced by food-insecure households was also associated with acute malnutrition in children. Infant and young child feeding practices, i.e., inadequate introduction of complementary foods and low dietary diversity to children were among the factors associated with nutritional status (P = 0.007). Among mothers, 87.5% had heard of malnutrition, 66.5% did not recognize the signs of malnourished in their children, and 92.4% were unaware of the consequences of malnutrition. Conclusion: Based on the results, initiatives and programmes should be established for women, the bearers of life, to enhance their empowerment and educate them with regard to the integral growth of children, the builders of tomorrow.