Background. The two major comrbidities (anemia and poor nutrition) are common manifestations of HIV-infected children, which threaten their lives. In Ethiopia, there is limited information on the magnitude and factors associated with anemia among HIV-infected children. Thus, this study was aimed to determine the magnitude and factors associated with anemia among HIV-infected children receiving antiretroviral therapy in the Afar region, Ethiopia. Methods. A cross-sectional retrospective record review was conducted on a sample size of 102 HIV-infected children aged 6 months to < 15 years in selected ART sites of the Afar region from May 1 to 25, 2018. Patient cards from 2009 to 2017 with the required information were considered. A paired sample t-test was used to assess whether there is a significant difference in the hemoglobin level before and after the HAART regimen. Multivariable logistic regression was used to determine predictors of anemia. Statistical significance was determined atp value < 0.05. Result. At baseline, 53.9% of study participants were anemic, from which 8.7%, 36.3%, and 9.8% were mild, moderate, and severe, respectively. There was a statistically significant improvement of hemoglobin level following the one-year course of ART treatment from 10.67 ± 1.82 to 11.5 ± 1.5 (p value ≤ 0.001): an improvement of 0.83 ± 1.74. Children who were moderately and severely stunted were more than five (AOR = 5.16, 95% CI (1.71, 15.56)) and more than twelve (AOR = 12.45, 95% CI (2.62, 59.21)) times more likely to be anemic than children who were not stunted, respectively. Children whose mothers had not attended ANC follow-up were more than three (AOR = 3.68, 95% CI (1.38, 9.81)) times more likely to be anemic than children whose mothers attended ANC. Children who were in clinical stages 3 and 4 were more than five (AOR = 5.07, 95% CI (1.79, 14.37)) times more likely to be anemic than children who were in clinical stage 1 and 2. Conclusion. The magnitude of anemia among HIV-infected children was found to be high, which is 53.9%. Nutritional status (stunting), WHO clinical stage, and history of ANC follow-up were the predictors significantly associated with childhood anemia. Thus, interventions for HIV-infected children should consider those factors.