Malignant thymoma, including thymic carcinoma, is extremely uncommon in the pediatric population. It is known to have a very poor outcome. We report on a 14-year-old boy with Epstein-Barr virus (EBV)-associated thymic carcinoma. Sections of the original tumor were analyzed for EBV by in situ hybridization to confirm the histological diagnosis of a lymphoepithelioma-like subtype. High copy numbers of EBV RNA were detected in the tumor tissue, suggesting an etiological role of EBV in our case. Intensive treatment resulted in long-term remission over 12 years. In order to facilitate the difficult management of the rare child with malignant thymoma, a literature search was initiated. Forty well-documented pediatric cases of malignant thymoma were found in the literature. Histological characteristics, clinical features, and therapeutic regimens were reviewed. Having the very limited experience with malignant thymoma in childhood in mind, it is concluded that its aggressiveness makes the most intensive treatment necessary. Long-term remission can be achieved by application of radical surgery, high-dose irradiation, and multiagent chemotherapy. The combination of cisplatinum, etoposide, and ifosfamide seems to be promising.