The double burden of malnutrition is an emerging nutritional problem of the coexistence of underweight and overweight. Obesity affects adolescents from both affluent and poor countries and nutritional status of adolescents in Ethiopia is not well documented, and they are the neglected segment of the population. The study aimed to assess prevalence and associated factors of double burden of malnutrition among adolescents in Burayu town, Ethiopia. A school-based cross-sectional study was conducted. A Stratified sampling was used to select a random sample of 627 adolescents from selected schools. Data on economic characteristics and socio-demographic information were collected by using an interviewer-administered questionnaire, and anthropometric measurements were made by using a digital Seca scale and height measuring board by trained data collectors. Data was entered into Epi-Data version 3.1 software and exported to SPSS version 24. World Health Organization Anthro-plus software was used to analyze anthropometric data. Both binary and multinomial logistic regression analyses was done to identify factors associated with the malnutrition of adolescents. Prevalence of stunting, thinness and overweight was 11.1, 3.9 and 12.1%, respectively. Having small number of children [AOR = 2.069, (95%CI: 1.161, 3.686)] significantly associated with stunting. Sex of adolescents [AOR = 4.454, (95%CI: 1.616, 12.278)], primary school adolescents [AOR = 0.233, (95%CI: 0.066, 0.821)] and secondary school adolescents [AOR = 0.229(95%CI: 0.056, 0.931)] and food sources [AOR = 3.750, (95%CI: 1.446, 9.728)] were significantly associated thinness. Sex of adolescents [AOR = 0.536, (95%CI: 0.318, 0.901)], school type [AOR = 0.326, (95%CI: 0.186, 0.571)] and number of children [AOR = 1.855, (95%CI: 1.086, 3.166)] were significantly associated overweight/obese. The study revealed the coexistence of double burden of malnutrition among in-school adolescents. There is an increasing trend in the level of stunting and overweight/obesity. Number of children that family had being associated with stunting and overweight/obesity. Food source and school level was positive association with thinness. School type and sex of adolescents associated with overweight/obesity.