Primary intracranial and sellar squamous cell carcinoma is an extremely rare entity, usually caused by malignant transformation of epidermoid cysts, or very rarely other non-malignant epithelial cysts. Malignant transformation of a Rathke’s cleft cyst has never been described. We present a 49-year-old male patient who presented with a 3-month history of progressive frontotemporal headaches. Imaging revealed a 1.2 cm cystic pituitary mass consistent with a hemorrhagic Rathke’s cleft cyst. The patient underwent trans-sphenoidal resection of the pituitary cyst, and pathologic analysis revealed a squamous cell carcinoma lining a Rathke’s cleft cyst. Extensive imaging and otorhinolaryngologic evaluation revealed no primary source for metastasis. We feel this represents the first case of a patient with a pituitary lesion in which presentation and MRI imaging were consistent with Rathke’s cleft cyst, yet histology revealed squamous cell carcinoma in situ.