The coexistence of both under nutrition and over nutrition or known as double burden of malnutrition (DBM) is a recent emerging nutritional problem documented in most developing countries. In Ethiopia, though there are various studies documenting the magnitude of under-five children nutritional problem, there is a research gap on DBM among adolescents. To fill the identified gap, the extent of the problem among in-school adolescents was assessed. A school based, cross-sectional study was conducted among 634 high school adolescent students in Arba Minch town, Southern Ethiopia from March 2015 to April 2015. Multi-stage sampling was employed to select the sampled participant. Following the school stratification by ownership as governmental and private, two schools were randomly selected from each category and the number of students were allocated proportionately. A pre-tested structured questionnaire was used to collect socio-demographic and anthropometric measurements. Weight, height, waist circumference and hip circumference measurements were taken from all participants using standard procedures. Data were entered into EPI-info version 7 and analyzed using SPSS, version21. The anthropometric data were converted into nutritional indices using WHO Anthro-Plus software, version 1.0.4. Both bivariate and multivariate analyses were done using multinomial regression model. A total of 406 from the government and 228 from the private schools were enrolled in the assessment. The magnitude of underweight, and overweight and/or obesity were 19.7% (95%CI: 16.5%, 23.2%), and 11.2% (95%CI: 8.7%, 13.7%), respectively. Father educational and occupation status, family size and wealth index were significantly associated with underweight. The odds of being underweight among whose fathers' had no formal education was 12 times [AOR=12; 95% CI=4 to 34], higher than those whose education level was above secondary. Those from family size of five or less were 80% times less likely to be underweight [AOR=0.2; 95% CI=0.12 to 0.4] than those whose family size was more than 5. Participants whose fathers' occupation was merchant were 75% times less likely to be underweight than private work [AOR=0.25; 95%CI=0.09 to 0.6]. Wealth index quintile of lowest [AOR=9.4; 95% CI=3 to 29] and second [AOR=5; 95%CI=1.8 to14.9] were 5 times more likely to be underweight than their counterparts. This study revealed the coexistence of double burden of malnutrition among in-school adolescents. Parents' education, family size and wealth index were some of the predictors which require the collaborative effort of health, education and social affair sectors to avert the prevailing problem in the community.