Key Clinical MessageFanconi anemia with Mitomycin C sensitivity is a rare, complex hematological condition. Our case study emphasizes the significance of early diagnosis, appropriate genetic testing, and cautious use of chemotherapeutic agents.AbstractFanconi anemia (FA) is a rare genetic disorder characterized by bone marrow failure, congenital anomalies, and predisposition to cancer. Here, we present the case of a 6‐year‐old boy with a known diagnosis of Fanconi anemia who exhibited sensitivity to Mitomycin C. The patient had a history of recurrent blood transfusions due to anemia and was referred to our institution following worsening symptoms, including pallor, swelling in limbs, and respiratory distress. Physical examination revealed characteristic features of FA such as mesomelia, low‐set ears, hyperpigmented macules, microcephaly, micropthalmos, and thumb hypoplasia. Imaging studies demonstrated bilateral radial hypoplasia and congenital agenesis of the left kidney. Laboratory investigations revealed pancytopenia, aberrant liver function tests, and elevated inflammatory markers. Importantly, the patient exhibited sensitivity to Mitomycin C, highlighting the necessity for caution in selecting chemotherapeutic agents in FA patients. This case underscores the importance of early recognition, comprehensive evaluation, and tailored management strategies of patients with Fanconi anemia to optimize outcomes and minimize complications.