BACKGROUND Myoepithelioma is a rare neoplasm that differentiates toward myoepithelial cells. This condition mainly occurs in the salivary gland and rarely in the soft tissue or internal organs. Long-term survival with repeated multiple rounds of resection for recurrence is rarely reported. CASE REPORT A 69-year-old man was diagnosed with metachronous pancreatic and thyroid metastases from myoepithelioma, which initially originated from a resected soft-tissue lesion in the left clavicular region in 2007. In addition, a locally recurrent lesion was resected and the patient received brachytherapy in 2015. Moreover, a metachronous metastatic lesion in the right lung was resected in 2017. Histopathological examination confirmed that all lesions were myoepithelioma. In the present case, pancreatoduodenectomy and right hemithyroidectomy for both metastatic lesions were successfully performed. Histopathology revealed small round-to-spindle-shaped tumor cells with atypia, proliferating in reticular formation, accompanied by myxoid stroma with chondromyxoid and hyalinized stroma, and the histology was similar to that observed in the previous specimen. Immunohistochemistry revealed positivity for cytokeratin (AE1/AE3), glial fibrillary acidic protein, vimentin, and S-100, and confirmed the diagnosis of myoepithelioma. To the best of our knowledge, this is the first study presenting a long-term survivor of soft-tissue myoepithelioma who underwent repeated multiple rounds of resection for recurrence in various organs. CONCLUSIONS We reported the case of a long-term survivor of soft-tissue myoepithelioma requiring multiple rounds of surgical resection for local recurrence and metachronous metastases in the lung, pancreas, and thyroid. When managed appropriately, some patients might benefit in terms of survival from repeated resection of recurrent lesions.