Background. Malnutrition among adolescents is a global public health problem. Nutrient intake is a proxy measure of nutritional status, but studies in developing countries describing the actual nutrient intake condition associated with nutrition in the adolescents are limited. On top of this, there is inconsistent finding on the extent of malnutrition among adolescents. Hence, the aim of this study was to assess malnutrition and the associated factors among adolescents at Dessie high school. Methods. A school-based cross-sectional study was conducted among 365 randomly selected high school adolescents. The data were collected using a structured questionnaire adapted from previous literature studies. Nutrient intakes were estimated by ESHA food processor software from a 24-hour recall, and anthropometric indices were calculated from weight, height, age, and sex. The data analysis was managed by SPSS version 23. Binary logistic regression and multinomial logistic regression were used to report the associated factors of malnutrition. Adjusted odds ratio with 95% CI was used to reveal the presence of statistical association. Results. The percentage of being stunted, underweight, and overweight/obese was 15.7%, 6.3%, and 8.2%, respectively. Snack consumption (AOR = 0.38, 95% CI: 0.20, 0.71) was negatively associated with stunting, while MAR <1 (AOR = 3.36, 95% CI: 1.15, 7.82) was positively associated with stunting. Being a male (AOR = 2.76, 95% CI: 1.03, 7.44) and meal consumption <3 times per day (AOR = 4.21, 95% CI: 1.35, 13.11) were factors positively associated with being underweight/thin. Dietary diversity score <5 (AOR = 0.35, 95% CI: 0.13, 0.89) was negatively associated with overweight/obesity, while MAR < 1 (AOR = 3.14, 95% CI: 1.09, 9.09) was positively associated with overweight/obesity. Conclusion. The percent of overweight/obesity among adolescents in the study area was higher compared with the national and regional prevalence, and this was found to be a public health concern. Therefore, increasing snack consumption, sex consideration, increasing meal consumption, and intake of diversified foods should be included in the prevention strategies of malnutrition among adolescents.