Abstract Background Spontaneous intracystic hemorrhage of cystic thymoma is very rare. We encountered a patient with giant cystic thymoma with spontaneous intracystic hemorrhage and successfully resected the thymoma. Case presentation A 38-year-old man was referred to our hospital with chest pain. Computed tomography revealed a uniform anterior mediastinum cystic mass. Two days after hospitalization, his chest pain worsened. Subsequent computed tomography showed that the tumor had become inhomogeneous. The patient’s symptoms gradually improved over a fortnight, and surgery was performed. The tumor was a cystic mass with a thick fibrous capsule filled with hemorrhagic necrotic tissue and was diagnosed as a cystic thymoma. Conclusions Mediastinal cystic lesion with expansion or contrasting effects in the wall may be a cystic thymoma, and it has the possibility of hemorrhaging in the cyst. In such a case, surgical resection is recommended.