Background: Optimal cognitive, emotional development and physiological function in children and adolescents requires access to food of adequate quantity and quality at all stages in life. Recurrent food insecurity as experienced in Ethiopia may result in malnutrition with resulting developmental impairments such as poor learning capacity in children. Stunting is fundamental factor which resulted in delayed cognitive development and under achievement of academic performance later in children‟s life at school. They are numerous study related to the magnitude and consequences of under-nutrition from different parts of the globe, but its relationship with educational achievement were not properly investigated and requires further investigation. Objective: To assess the association between stunting and school performance among primary school children, Dera woreda, northwest Ethiopia Methods: School based cross-sectional study was conducted from September 20-October 5, 2019 .Simple random sampling techniques were used to select a total of 337 study participants. Data were collected by using a pre-tested structured questionnaire, height was measured by stadiometer and academic performance data were collected from school roster. Then the data entered into SPSS version 23 for analysis. WHO AnthroPlus software was used to calculate the Z-score of height-for-age of children and multivariable logistic regression analysis were employed to control the effect of potential confounders. Variables with a p- value<0.05 in the multivariable model identified as predictors of school performance. Result:-.The mean academic performance for study participants was 65.54(±13.63SD). The prevalence of stunting was very high 47.6% with 95%CI. The regression result of this finding generally shows that age 9-10 (OR=11.458) and 11-12(OR=12.916) have positively significant relationship with 90-100, Eating breakfast (OR=0.153) has negatively significant relationship to achieve 80-89 and workload (OR=0.429) has negatively relationship with 60-79 to achieve academically. Conclusion: Academic performance was varying among sex; male students perform academically better than females. Academic performance was also varying among monthly income, the higher average monthly income the better achiever. Even though HAZ are not statistically significant relationship with academic achievement, the prevalence of stunting among study participants was high and varies among sex; males were highly stunted than females.