Fanconi anemia (FA) is a type of bone marrow failure syndrome based on an autosomal recessive inherited trait with increased predisposition for other cancers. It is extremely rare and is characterized by short stature, polydactyly, and pancytopenia. At present, the only effective treatment for FA is allogeneic hematopoietic stem cell transplantation (SCT). Chemotherapy is necessary prior to allogeneic SCT. Dental treatment is usually performed before chemotherapy to reduce potential infections. We experienced the anesthetic management of a 4-year-old boy diagnosed with FA, who underwent extensive dental extractions before chemotherapy for SCT. In the preoperative examination, the platelet count was decreased to less than 3.0 × 10⁴ cells/μL because of chronic pancytopenia. The patient received 20 units of platelet transfusion over 3 days prior to anesthesia. Dental surgery and multiple dental extractions were successfully completed under general anesthesia with sevoflurane, fentanyl, and remifentanil, and chemotherapy started 3 days postoperatively.