We report on a 50-year-old female who developed pulmonary metastasis 12 years following the resection of a thymoma with microscopic capsular invasion. The patient was found to have a mediastinal mass at the age of 18 years; however, she refused to undergo surgery. At the age of 38 years, the patient underwent surgery for resection of the tumor; it was diagnosed as a macroscopically encapsulated thymoma with microscopic capsular invasion. Multiple pulmonary metastases occurred 12 years following the resection of the tumor; all the metastatic masses were resected. Although the patient suffered from myasthenia gravis 4 months following the resection of pulmonary metastases, she remains free of myasthenia gravis with no recurrence of tumor at 2 years post-surgery. Long-term follow-up is essential for the detection of recurrence after resection of a thymoma with microscopic capsular invasion, and surgery could be the best treatment for distant metastasis in case of resectable lesions.