Background: Congenital hemolytic anemia (CHA) is a group of monogenic diseases presenting with anemia due to increased destruction of circulating erythrocytes. The erythrocyte abnormalities are classified into three major disorders of red cell membrane defects, hemoglobinopathies, and red cell enzymopathies. The clinical manifestations of CHA are anemia, jaundice, cholelithiasis, and splenomegaly, while the onset mode and severity are both variables. Howsoever, diagnosis of CHA is a challenge because clinical features are similar in cases with different etiologies and it is difficult to distinguish between them using conventional diagnostic techniques. Recent advances in genetic testing approaches such as next‐generation sequencing have made diagnosis more accurate and quicker. Thus, the aim of our study is to evaluate the feasibility of a custom panel based on NGS Technology for sequencing of the genes associated with CHA. Aims: We aimed to enhance the diagnosis of patients with congenital anemias by using targeted next‐generation sequencing panel and also to establish a genotype‐phenotype correlation with clinical manifestations of the disease. Methods: Genetic diagnosis was performed by gene capture followed by targeted next‐generation sequencing which includes gene related to congenital anemia. Thirty‐five patients with unexplained congenital anemia were enrolled for NGS analysis. Further validation of variants was confirmed by Sanger Sequencing. Results: In the test group, we identified pathogenic mutations in 29 cases: Seven had a variant in the HBB gene which was misdiagnosed due to interference of transfused blood; fourteen had pathogenic mutations in genes related to RBC enzymopathies‐ PKLR (p.I282S, p.V294 M, p.D331G,p.G332S, p.R449G, p.I494T, p.V506I, p.W525X),GPI(p.R347H), HK( p.T905K), AK1(p.Q24R, p.R138H), large base deletion in P5’N gene; one had novel homozygous mutation in C15orf41 gene (p.V84E) associated with CDA1b, three had presented with mutation in ribosomal proteins RPL5 (p.D234G), RPL26 (p.M115T), RPL27 (p.I25T) which is a diagnostic variant of Diamond Blackfan Anemia and one variant in each gene FANC1 (Fanconi anemia), ABCG8 (Sitosterolemia), LRBA (autoimmunity, lymphoproliferation, and immune deficiency) and, RTEL1 (Dyskeratosis congenital) were identified. Summary/Conclusion: Targeted next‐generation sequencing led to an accurate diagnosis in over 82% of patients with rare anemias. Earlier incorporation of this method into the workup of patients with congenital anemia may improve patients care by offering specific therapeutic approaches and enable genetic counseling.