We report a case of basaloid carcinoma originated from the wall of a large thymic cyst, which is a very rare subtype of thymic carcinoma. A 60-year-old man admitted at our hospital due to dyspnea with pericardial and left thoracic effusion on chest X-ray. A computed tomography and a magnetic resonance imaging demonstrated a large anterior mediastinal cyst and a small mass lesion on the part of the wall. We performed as possible as resection of the thymic cyst and the tumor with median sternotomy. The pathological diagnosis was a thymic basaloid carcinoma originated from the wall of a thymic cyst, which classified into a low-grade histology in thymic carcinoma. He has been well with no evidence of recurrence for three years since operation followed by a post-operative radiation therapy (total 57 Gy) to the residual tumor and mediastinum.