Introduction malnutrition is a major public health issue affecting adolescents globally and developing countries in particular. Adolescent period is very sensitive to malnutrition. Adolescent malnutrition can be affected by different factors. The objective of this study was to assess prevalence and associated factors of adolescent malnutrition among high school students. Methods an institutional-based cross-sectional study was carried out among school adolescents in Durame town high schools. Of the 498 selected school adolescents, 455 (91.4 %) were included in this study. Data were entered into Epi data and exported to World Health Organization (WHO) Anthroplus and Statistical package for the social sciences (SPSS). Odds ratio at 95% confidence interval (CI) was calculated to check for the existence and strength of association between variables. P-value less than 0.05 was used to declare significance of association. Results the prevalence of stunting, thinness and overweight among adolescents was 26 (5.7%), 11(2.4 %) and 42 (9.2%), respectively. Residing in rural (AOR=5.31, 95% CI: 1.03-27.27) and utilize community based nutrition (AOR=0.26, 95% CI: 0.07-0.98) were associated with thinness. Male (AOR=3.55, 95% CI: 1.62-7.81) and having cattle (AOR=2.78, 95% CI: 1.393, 5.565) were associated with overweight. Conclusion around two in twenty-five adolescents are stunted. About one in twenty-five adolescents are thin. More than two in twenty-five adolescents are overweight. Sex of adolescents, having cattle were associated with overweight of adolescent. Rural residence and utilizing community based nutrition were associated with thinness. Minister of Health and other health offices should implement nutrition education to school adolescents by giving emphasis on place of residence and for both male and female adolescents.