A newborn girl presented with massive proptosis of the right eye. Physical and radiologic examination disclosed that the primary orbital mass was confined to the site. A diagnosis of malignant rhabdoid tumor was made by histopathologic examination of an incisional biopsy specimen. Exenteration was performed, and the resection margins were free from tumor cells. However, distant metastasis developed in the liver 1 month after surgery. Despite chemotherapy, the patient died 2 months later due to tumor invasion into the central nervous system, which was confirmed by autopsy. To the best of our knowledge, this is the first case of congenital orbital malignant rhabdoid tumor showing systemic metastasis after exenteration, which suggests the need for aggressive systemic treatment rather than exenteration, even in a case of locally confined tumor.