Fanconi anemia is a recessively inherited disease, characterized by various anomalies, bone marrow failure, and a predisposition to acute myeloid leukaemia and squamous cell carcinoma. The disease is caused by mutations in one of the 13 currently known Fanconi anemia genes involved in the repair of DNA breaks. Squamous cell carcinomas arise chiefly in the oral cavity, but also in the anogenital region, mostly at relatively young age. Managing the carcinomas is difficult since the patients have are extremely sensitive to treatments such as radiation and chemoradiation using cisplatin. Therefore, early diagnosis and early surgical intervention are the best approaches. Human papillomavirus may play a role in the etiology of the oral squamous cell carcinomas, but current research results are inconsistent. Human papillomavirus vaccination and non-invasive screening for premalignant lesions, combined with frequent clinical examinations and early surgical treatment should improve the prevention and prognosis of these tumors in Fanconi anemia patients.