Background: Although the adolescences are a window of opportunity to break the intergenerational cycle of malnutrition, they are the neglected age groups. This study aimed to assess the prevalence and associated factors of stunting and thinness among school adolescents in Finoteselam town, Amhara region, Ethiopia, 2018. Methods: A school-based cross-sectional study among adolescent students aged 10-19 in public primary and secondary schools was carried out in Finoteselam town from February to March, 2018. A stratified random sampling technique was employed to select study subjects. Pre tested structured questionnaires were used to collect the data. Data was entered using Epi info version 7 and analyzed using SPSS version 20 and WHO Anthro Plus soft ware. A multivariate logistic regression analysis was employed to identify factors associated with stunting and thinness. Crude and adjusted odds ratios with 95% level significance were used to measure the strength of association and statistical significance was declared at p-value less than 0.05. Results: The prevalence of stunting and thinness among adolescents was 21.8% and 16.9% respectively. Being male (AOR= 2.27; 95% CI 1.32, 8.13), coming from rural area (AOR= 2.38; 95% CI 109, 5.18) and having less than 1000 birr family monthly income (AOR= 2.61; 95% CI 1.04, 6.50) were significantly associated with stunting at P-value <0.05. Early Adolescent stage (AOR= 4.81; 95% CI: 1.23, 18.51), being Male adolescent students (AOR = 2.33; 95 % CI: 1.60, 3.40), having less than 1000 birr family monthly income (AOR= 6.54; 95% CI: 3:82, 14.89), having 1000-2000 birr family monthly income (AOR= 3.47; 95% CI: 1.15, 7.45), using well water (AOR= 3.82; 95% CI: 1.46, 10.04) and having less than four dietary diversity (AOR = 2.24, 95 % CI: 1.32, 8.13) were significantly associated with thinness at P-value <0.05. Conclusion and Recommendation: The study showed that the prevalence of stunting was medium, but the prevalence of thinness was critical. Sex, place residence and family monthly income were found to be important factors associated with stunting and thinness among the respondents. Further analytic studies were recommended to identify unexplored underlying causes of stunting and thinness among adolescents.