Salivary duct carcinoma is a malignant salivary neoplasm with a poor prognosis. Effective treatment for remote metastases has not been recognized. We report herein on a case of this tumor overexpressing HER2 successfully treated with trastuzumab-based molecular targeted therapy. The patient was a 69-year-old man, who developed remote metastases into the liver and the thoracic vertebra six months after surgery and postoperative irradiation for the primary and nodal lesions. After targeted therapy including paclitaxel and trastuzumab, these metastatic lesions showed rapid and continued regression. After paclitaxel was discontinued due to peripheral neuropathy in the extremities, trastuzumab monotherapy followed without resulting in cardiotoxicity. After three years since development of remote metastases, the patient is doing well without re-progression of the disease.