Objective: This kind of study was conducted first time in Pakistan. Its objective was to ascertain the associated clinical features and analyze the FANCA exon 28 and exon 29 mutations in Pakistani Fanconi anemia (FA) patients. Methods: A total of 38 patients with Fanconi anemia were recruited presenting in the Armed forces institute of pathology (AFIP) Rawalpindi Pakistan. They were enrolled in this study on the basis of comprehensive clinical evaluation and positive Diepoxybutane (DEB)/Mitomycin C Chromosomal breakage test. Genomic DNA was extracted from peripheral blood of patients and age and gender-matched controls. Mutation analysis of FANCA gene was done by conventional Polymerase chain reaction (PCR) and DNA sequencing. Various online tools and software were used for analysis of the obtained data and identification of the sequence alterations in FANCA gene in exon 28 and exon 29 of FA patients. Results and Discussion: The current study on screening of FANCA mutational analysis in exon 28 and exon 29 revealed four novel mutations. These include three missense variants (p.F876L, p.L883H, and p.K921I) in exon 28 and a novel homozygous frameshift variant (p.S947FfsX950) in exon 29. In addition two new intronic variants were also found in this set of patients. Conclusion: The sequence variants identified in this study in 10 (26.31%) FA patients in two out of forty-three FANCA gene exons (i.e., exon 28 and exon 29) strongly emphasize the importance of large-scale molecular studies on FANCA gene in Pakistani population.