Fanconi anemia (FA) is an inherited bone marrow failure syndrome characterized by pancytopenia, physical abnormalities and predisposition to malignancy. It is due to DNA repair defect results in genomic instability. Diagnosis is done by chromosomal fragility test which is high sensitive and low specific test. In this case report, a nine year old girl was accidentally identified with bicytopenia during febrile illness with reactive bone marrow initially. It was followed by pancytopenia with hypocellular marrow. She was diagnosed as FA with classic physical findings of café au lait spots, microcephaly, torticollis, hypocellular bone marrow, positive mitomycin-C stress cytogenetic test and high HbF.