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Abstract A 72‐year‐old man was diagnosed as having myasthenia gravis (MG). He underwent computed tomography which revealed an anterior mediastinal tumour. Laboratory examination revealed elevated levels (106.3 U/ml) of carbohydrate antigen (CA) 19‐9 in serum. However, no malignant disease was detected on fluorodeoxyglucose‐positron emission tomography. A diagnosis of thymoma associated with MG was considered and an extended thymectomy was performed. Histopathologically, thymoma was categorized as stage I based on the Masaoka classification, and as type AB according to the World Health Organization classification. Immunohistochemistry was positive for CA 19‐9. The serum levels returned to the normal range post‐operatively (16.7 U/ml). Herein, we report an extremely rare case of thymoma with raised levels of CA 19‐9.