We report a 60-year-old male with thymoma-associated myasthenia gravis with anti-MuSK antibodies. In October 2010, he had diplopia, ptosis, and dysphagia. He was diagnosed to have MG in February 2011. The neurological examination disclosed external ophthalmoplegia, bilateral ptosis, mild dysphagia, and fatigability. Repetitive nerve stimulation of the right facial nerve showed CMAP decrement greater than 10%. Patients showed an improvement in ptosis after administration of edrophonium.Anti-acetylcholine receptor antibody was negative, and anti-muscle specific receptor tyrosine kinase antibody was 66.8 nmol/l (cut-off value: 0.05 nmol/l). Prednisolone (50 mg every other day) were started. Contrast-enhanced chest MRI showed a mediastinal mass suggestive of thymoma. Extended thymectomy was performed in March 2011. Histological examination disclosed a type B1 thymoma. After resection of the tumor, the symptoms of MG improved with prednisolone (100 mg every other day). This is a rare case of MG with anti-MuSK antibodies and thymoma, which has been reported previously only in 2 cases.