Fanconi anemia is a rare genetic disorder affecting various body systems. Congenital abnormalities, poor hematopoiesis, a higher incidence of acute myeloid leukemia, myelodysplastic syndrome, and malignancies are the hallmarks of this autosomal recessive condition. In certain instances, the clinical signs and highly diverse phenotypic presentation make a diagnosis challenging. In this case report, an eight-year-old boy presented with recurrent episodes of fever, generalized weakness and physical deformities. He had left thumb deformity, triangular face, short stature, and hyperpigmentation with café au lait spots. Bone marrow biopsy revealed hypoplastic marrow, peripheral blood smear revealed pancytopenia, and chromosomal breakage testing was also positive.