Fanconi anemia (FA) is a rare inherited disorder marked by genomic instability, progressive bone marrow failure, congenital anomalies, and heightened cancer susceptibility. It results from mutations in genes involved in the FA/BRCA DNA repair pathway. FA diagnosis relies on chromosomal breakage assays and genetic testing, though somatic mosaicism and overlapping syndromes can complicate detection. Hematopoietic stem cell transplantation (HSCT) remains the only curative therapy for bone marrow failure and clonal evolution, with outcomes significantly improved through reduced-intensity conditioning and donor-matching strategies. Emerging options include haploidentical HSCT and gene therapy (GT). FA patients face increased risks of myeloid malignancies and solid tumors, particularly head and neck squamous cell carcinoma (HNSCC). Therefore, early surveillance, multidisciplinary care, and transplant timing are essential to optimize survival and reduce complications. Continued advances in genetic understanding, targeted therapies, and early diagnosis are critical to improving outcomes for individuals affected by FA.