Either metastatic or primary squamous cell carcinoma in the gastrointestinal tract is extremely rare, with very few cases reported in the literature. In this paper, we report a case in which the patient presented with dysphagia during the course of radiotherapy for recurrent lung cancer in a mediastinal lymph node. Although the dysphagia mimicked radiation esophagitis, the ultimate cause proved to be gastric and duodenal metastases from primary lung squamous cell carcinoma. Taking into account the value of identification of metastatic or primary SCC in the stomach and duodenum on the prognosis and treatment options, it is imperative that the correct diagnosis be established. This report is followed by a discussion of the differential diagnosis between metastatic and primary squamous cell carcinoma in the stomach and duodenum.