Introduction. Congenital heart disease (CHD) is the most common birth defect. Anemia is the prevailing manifestation of micronutrient deficiency. It has been demonstrated that anemia in children increases morbidity and has a negative impact on psychomotor development. Despite its negative consequences, which have been documented for a long time in clinical practice, the issue does not gain sufficient attention in developing countries, specifically in children with CHD. Thus, this study is aimes to assess the prevalence of anemia and the factors associated in children with CHD. Methods. Institutional-based cross-sectional study was conducted on CHD children at selected governmental hospitals in Addis Ababa, Ethiopia, from February to March 2021. During this period, 373 children with acyanotic and cyanotic heart disease between 0 months and 15 years of age were included in this study. All children were assessed using structured questionnaires and anthropometric measurements. Recent hemoglobin results that are avaliable in the medical charts of children were used to diagnose anemia. The data were analyzed using SPSS version 25. Results. From randomly included 373 children with CHD, 298 (79.9%) had acyanotic congenital heart disease (ACHD) and 75 (20.1%) had cyanotic congenital heart disease (CCHD). Twenty-five (33.3%) CCHD and 192 (64.4%) ACHD cases of children were malnourished. The most common type of CCHD and ACHD defects were ventricular septal defects and tetralogy of fallout, respectively. Overall, the prevalence of anemia in ACHD and CCHD was 24.5% and 72%, respectively. In children with ACHD, the frequency of anemia was reported to be significantly higher in the malnourished group than in the well-nourished. Conclusions. A high prevalence of anemia is observed in children with CHD. This study highly suggests further evaluation to determine the frequency and complications of blood indices and other hematological impairments in ACHD, CCHD, and children with both problems. Moreover, the findings of this study on illness profiles in children with CHD prompt further research into the cellular and molecular mechanisms underlying immune system dysfunction.