Fanconi anemia is a recessive autosomal syndrome characterized by congenital abnormalities, low stature, bone marrow failure, and higher susceptibility to malignancies, including oral. The Hematopoietic Stem Cell Transplantation (HSCT) and Graft versus Host Disease (GVHD) seems to increase the risk of oral malignant transformation.In 2009, a 36-year old female patient with Fanconi anemia diagnosis was evaluated at the Bone Marrow Unit of Hospital de Clı́nicas from Universidade Federal do Paraná in Brazil, complaining of a 1year evolution painful injury in the palate. The patient reported not being a smoker and denied any alcohol drinking habits. She had completed one year and eight months of a related HSCT. Clinical examination showed red erosive lesions in the hard palate, compatible with chronic GVHD. Dexamethasone and nistatin rinse were prescribed five times a day in addition to the GVHD systemic treatment protocol. Six months later, the patient returned with more intense oral GVHD, with erosion and ulcers throughout the palate and complained of a nodular lesion on right tongue border, which was preventing an adequate oral hygiene. At clinical evaluation, the lesion had firm consistency, red coloration similar to the normal adjacent mucosa, and approximately three centimeters. An incisional biopsy was performed and the histopathology revealed a Squamous Cell Carcinoma (SCC). The patient was referred to a head and neck surgeon and was submitted to a partial glossectomy. No radiotherapy and chemotherapy were indicated. The patient died due to post-operatory complications.Patient’s age and post-HSCT elapsed time are important risk factors for SCC development in patients with Fanconi anemia. A thorough and periodical oral examination is indicated in post FA patients to identify possible initial potentially malignant lesions.