The author herein reports a very rare case of pure small cell carcinoma of the esophagus with an emphasis on KIT and PDGFRA. A 72-year-old man was admitted to our hospital because of dysphagia, and endoscopy showed a tumor in the esophagus. A biopsy of the esophageal tumor showed a small cell carcinoma consisting of malignant small cells with very hyperchromatic nuclei and inconspicuous nucleoli and without any differentiations. An immunohistochemical study revealed positive reaction for cytokeratin (Dako, Glostrup, Denmark), KIT, PDGFRA, synaptophysin, p53 protein, and CD56, and negative reaction for chromogranin, CD45, CD20, CD3, and CD30. The Ki-67 labeling was 95%. A molecular genetic analysis showed no mutations of KIT and PDGFRA genes. The patient underwent radiation (50 Gray) and chemotherapy (cisplatin, 5 courses), but he developed liver and bone metastases and died of systemic carcinomatosis five months after the initial presentation.