Introduction: Anemia among reproductive age group women in Ethiopia is moderate public health problem. However, the prevalence of anemia among school going adolescent girls is not well documented yet. Objective: To determine the magnitude of anemia and associated factors among school going adolescent girls in Berahle district, Afar, northeast Ethiopia. Methodology: Institutional based cross-sectional study design was employed. Multi-stage sampling technique was used: In first stage schools were selected randomly, in the second stage in the selected schools, 338 school going adolescent girls (age 14-19 years old) were selected systematically. Structured questionnaires was used to collect Socio-demographic, socio-economic, dietary pattern and frequency of study participants. After collecting the Blood sample, Hemocue haemoglobin spectrophotometer (Hemocue HB 301 analyzer) was used to analysis hemoglobin concentration. SPSS version16.1 statistical software was used to enter and analysis the data. Bivariate and multivariate logistic regressions were used to test association among dependant and independent variables. For all statistical tests, significance level was set at p-value of 0.05 and confidence interval of 95%. Result: Around one-fourth (22.8%) of school going adolescent girls were anemic. Low Scio Economic States, AOR 2.8 (CI: 1.1, 3.7), not consuming egg AOR 2.4 (CI: 1.3, 4.3), milk consumption AOR 7.2(CI: 2.9, 17.6), not consumption of vegetables AOR 2.5 (CI: 1.3, 4.9) and meat AOR 2.4 (CI: 1.24, 4.67) were the significant causes for aneamia. Conclusion: Anemia among school going adolescent girls was moderate public health problem and Low Scio-economic States, low consumption of egg, meat and other vegetables and high consumption of milk were the significant causes for anemia.