Primary intrapulmonary thymoma is a rare lesion with around 20 cases reported so far in the literature. A pure spindle cell morphology in these lesions is rarer still with only a single case recorded to date. We report herein an interesting case of a 47-year-old-man, status post surgical resection and radiotherapy for a squamous cell carcinoma of the floor of mouth, who was being followed up for a radiologic opacity in the right lower lobe of the lung. The lesion remained stable in size for almost 5 years and then an increase in size was noted. A right lower lobectomy was performed with a preoperative suspicion of metastasis. Histologic and immunohistochemical evaluation revealed a primary intrapulmonary spindle cell thymoma that displayed a prominent granulomatous reaction, a phenomenon not described so far in the literature. We discuss the possible embryologic origins and the pitfalls in diagnosis of these rare neoplasms. The remarkable granulomatous response observed in the tumor raises the possibility that similar lesions might conceivably occur in the thymus as well.