Background: Fanconi anemia (FA) is a rare inherited bone marrow failure syndrome marked by chromosomal instability, congenital anomalies, and progressive pancytopenia. Early diagnosis is crucial due to increased risk of hematologic malignancies and multi-system involvement, particularly in populations with high rates of consanguinity. Objective: This study aimed to describe the clinical characteristics and disease outcomes of pediatric patients with Fanconi anemia managed at a single tertiary care center in Egypt. Patients and methods: A retrospective review was conducted on medical records of 46 children diagnosed with FA between January 2005 and December 2021 at the Pediatric Hematology Clinic, Ain Shams University Children's Hospital. Diagnosis was confirmed by clinical features and chromosomal breakage analysis using diepoxybutane (DEB). Demographics, clinical presentation, laboratory data, bone marrow findings, cytogenetics, treatments, and outcomes were analyzed. Results: Among the 46 patients, 65.2% were male, and 84.4% had parental consanguinity. Recurrent infections were documented in 43.5%, with no cases of acute myeloid leukemia at diagnosis. Somatic anomalies included microcephaly (58.7%), short stature (55.8%), and skin pigmentation (47.8%). Bone marrow hypocellularity was present in 95% of cases (n=40/42), while dysplastic changes were seen in 20.5% (n=9/44). Cytogenetic analysis revealed a 1q+ abnormality in 2.2% of patients. Conclusion: This study highlighted the high burden of congenital anomalies and bone marrow failure among Egyptian children with FA, compounded by high consanguinity rates. These findings underscored the need for early diagnosis, genetic counselling, and access to curative therapies like stem cell transplantation.