The clear cell variant of oral squamous cell carcinoma (CCSCC) is an uncommon aggressive lesion found in the oral cavity. Limited cases of CCSCC have been documented in the literature. This report discusses a 38-year-old female presenting with a non-healing ulcer in the right retromolar region, accompanied by pain and discomfort. Histopathological analysis revealed sheets and islands of severely dysplastic epithelial cells with clear cytoplasm and keratin pearls within the connective tissue, indicating a rare variant of oral squamous cell carcinoma. Various differential diagnoses were kept in mind, and a series of histopathological, histochemical, and immunohistochemical markers were carried out to confirm the origin of these clear cells. It was positive for cytokeratin 8, cytokeratin 18, and cytokeratin cocktail (AE1/AE3). It was negative for vimentin, S100, and HMB45. Thus, our final diagnosis was a CCSCC. This variant is seldom encountered. It often presents diagnostic challenges and is also an enigma to understanding its biological behavior.