Background: Malnutrition is a major public health concern that affects health, growth, development, and academic performance. Though evidence about the magnitude of undernutrition is well established in Ethiopia, there is scarcity of research findings that clearly assess undernutrition in primary school children with relating to academic performance. Objective: To assess prevalence of undernutrition, its association with academic performance and factors associated with undernutrition among primary school children living in Dessie Town. Methods: Institution based cross sectional study was conducted among 472 primary school children from February to April 2018 in Dessie Town, Ethipia. A multi stage sampling technique was employed to select the study participants. The data were collected by using interviewer administered questionnaire and entered to EPI-INFO version 7 software and analysis was made by using SPSS Version 20 software. Anthropometric data was analyzed by using WHO Anthro Plus Version 1.0.4 software. Spearman correlation analysis was performed to determine correlation between academic performance and undernutrition. Binary Logistic regression analysis was also performed with 95% CI to identify factors associated with undernutrition. Results: Prevalence of stunting and thinness in this study were 21.5% and 14.4% respectively. There was a significant positive correlation between stunting with academic performance and semester mathematics result (r=0.255, p<0.001) and (r=0.327, p<0.001) respectively. Multiple logistic analysis indicated that mother’s educational status [AOR=8.95; 95% CI (4.51, 17.75)], family monthly income [AOR=3.93; 95%CI (1.96, 7.91)], house floor made of soil [AOR=2.51; 95% CI (1.36,4.36), children born from mothers younger than 20 years [AOR=3;95% CI(1.09,8.29)] were factors significantly associated with stunting. The risk of thinness increased significantly with having family ≥7 members [AOR 11.58; 95% CI (4.04, 33.16)] live in house floor made of soil [AOR 2.27; 95% CI (1.08, 4.74)], having meal frequency ≤3 times a day [AOR 3.14; 95% CI (1.35, 5.69)], and history of illness in two weeks prior to the survey [AOR 2.42; 95% CI (1.24, 5.80)]. Conclusion and recommendations: Stunting and thinness was prevalent. Stunting was found to be correlated with academic performance and mathematics result of students. Policy makers should consider school age children in their nutrition policy documents and implement screening program and intervention strategy.