The author reports herein an extremely rare case of primary small cell carcinoma of the mediastinum with an emphasis on KIT and PDGFRA genes. A 66-year-old man was found to have a mediastinal tumor on a routine chest X-ray examination, and was admitted to our hospital. Imaging modalities revealed a 5 × 4 cm tumor in the middle mediastinum near the bronchial carina. No other tumors were detected in the body including the lungs. Video-assisted thoracoscopy confirmed the mediastinal tumor, and a large incisional biopsy was performed. The tumor was histologically small cell carcinoma. An immunohistochemical study revealed positive reactions for cytokeratins (AE1/3, polyclonal), synaptophysin, neuron-specific enolase, CD56, KIT, and PDGFRA, and negative reactions for chromogranin, CEA, CD45, CD20, and CD3. Ki-67 labeling showed a value of 80%. A molecular genetic analysis using PCR-direct sequencing identified no mutations of KIT (exons 9, 11, 13, and 17) and PDGFRA (exons 12 and 18) genes. The patient received radiation and chemotherapy, and the tumor was fully resolved. The patient has remained free of recurrence for 6 years after the first presentation. The present case is the first reported case of primary small cell carcinoma of the mediastinum with an examination of KIT and PDGFRA expressions and KIT and PDFGRA gene mutations.